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Restructuring and updating test data of locarna tool (#1481)
* Updating tools/rna_tools/locarna from version 1.9.2.3 to 2.0.1 * Restructured locarna_exparnap tool * Updated locarna_multiple and associated test data * Restructured locarna_pairwise_p and related test data * Restructured locarna_pairwise and updated test data * Restructured locarna_reliability_profile and updated test data * Update tools/rna_tools/locarna/macros.xml --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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‎tools/rna_tools/locarna/locarna_exparnap.xml‎

Lines changed: 42 additions & 116 deletions
Original file line numberDiff line numberDiff line change
@@ -2,25 +2,18 @@
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<description>
33
Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
44
</description>
5-
65
<macros>
76
<import>macros.xml</import>
87
</macros>
9-
10-
<expand macro="requirements" />
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<expand macro="stdio" />
13-
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<expand macro="version" />
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8+
<expand macro="requirements"/>
9+
<expand macro="stdio"/>
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<expand macro="version"/>
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<command><![CDATA[
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exparna_p
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'$inputA'
2014
'$inputB'
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22-
## -------------------- scoring parameters
23-
#
16+
## -------------------- scoring parameters -------------#
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$Scoring.no_stacking
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--alpha_1 $Scoring.alpha_1
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--alpha_2 $Scoring.alpha_2
@@ -35,8 +28,7 @@
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@CONSTRAINT_ARGS@
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@FOLDING_ARGS@
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## -------------------- other parameters
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#
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## -------------------- other parameters---------------- #
4032
#if str($Other.subopt.subopt_selector) == "on"
4133
--diff-to-opt-score $Other.subopt.diff_to_opt_score
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--number-of-EPMs $Other.subopt.number_of_EPMs
@@ -49,7 +41,7 @@
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$Other.no_chaining
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--out-min-prob $Other.out_min_prob
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## -------------------- output
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## -------------------- output ---------------- #
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#if 'postscript' in str($outputs).split(",")
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--output-ps
@@ -79,7 +71,7 @@
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@STDOUT_ARGS@
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## -------------------- post processing
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## -------------------- post processing --------------#
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#if 'anchors-pp' in str($outputs).split(",")
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&& mv anchors_pp_A.pp '$anchors_ppA'
@@ -89,161 +81,95 @@
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]]></command>
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<inputs>
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<param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
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help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
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/>
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<param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
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help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
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/>
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<param name="outputs" type="select" display="checkboxes" multiple="true"
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label="Output options">
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<option value="postscript" selected="false">Best EPM chain
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as colored postscript</option>
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<option value="anchors-fasta" selected="false">Fasta with anchor
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constraints from chaining</option>
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<option value="anchors-pp" selected="false">LocARNA PP
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files merging input PPs and anchor constraints from
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chaining</option>
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<option value="clustal" selected="false">Chain as
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alignment in Clustal format</option>
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<param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
85+
<param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
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<param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
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<option value="postscript" selected="false">Best EPM chain as colored postscript</option>
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<option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
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<option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>
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<option value="clustal" selected="false">Chain as alignment in Clustal format</option>
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<option value="epm_list" selected="false">List of the found EPMs</option>
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<option value="chained_epm_list" selected="false">List of
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EPMs in the best chain</option>
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<option value="chained_epm_list" selected="false">List of EPMs in the best chain</option>
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</param>
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<param name="stdout_verbosity" type="select" label="Standard output verbosity">
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<option value="--quiet">Don't report standard
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output</option>
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<option value="--quiet">Don't report standard output</option>
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<option value="" selected="true">Non verbose</option>
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<option value="--verbose">Verbose</option>
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</param>
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<section name="Scoring" title="Scoring parameters">
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<param argument="--alpha_1"
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type="integer" value="1" min="0" max="50"
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label="Sequence score factor"
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/>
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<param argument="--alpha_2"
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type="integer" value="5" min="0" max="50"
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label="Structure score factor"
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/>
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<param argument="--no-stacking" type="boolean"
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truevalue="" falsevalue="--no-stacking"
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label="Add stacking terms"
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/>
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<param argument="--alpha_3"
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type="integer" value="5" min="0" max="50"
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label="Stacking score factor"
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/>
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<param argument="--struct-mismatch-score"
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type="integer" value="-10" min="-100" max="0"
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label="Score for nucleotide mismatch in base pair match"
142-
/>
100+
<param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
101+
<param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
102+
<param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
103+
<param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
104+
<param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
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</section>
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<section name="Folding" title="RNA folding parameters">
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<expand macro="common_folding_parameters" />
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</section>
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<section name="Heuristics" title="Heuristic parameters">
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<expand macro="common_heuristic_parameters" />
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<expand macro="max_diff_parameters" />
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<expand macro="in_loop_ratio_parameters" />
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<expand macro="exparnap_in_loop_parameters" />
154114
</section>
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156115
<section name="Constraints" title="Constraint parameters">
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<expand macro="common_constraint_parameters" />
158117
</section>
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161118
<section name="Other" title="Other parameters">
162119
<conditional name="subopt">
163-
<param name="subopt_selector" type="select"
164-
label="Suboptimal traceback of EPMs (exact pattern matches)"
165-
help="(--subopt)">
166-
<option value="off">Enumerate only optimal
167-
EPMs</option>
120+
<param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
121+
<option value="off">Enumerate only optimal EPMs</option>
168122
<option value="on">Perform suboptimal traceback of EPMs</option>
169123
</param>
170124
<when value="off" />
171125
<when value="on">
172-
<param argument="--diff-to-opt-score"
173-
type="integer" value="-1" min="-20" max="0"
174-
label="Maximum score difference to optimum" />
175-
<param argument="--number-of-EPMs"
176-
type="integer" value="100" min="1" max="10000"
177-
label="Maximal number of EPMs" />
126+
<param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
127+
<param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
178128
</when>
179129
</conditional>
180130

181-
<param argument="--min-score"
182-
type="integer" value="30" min="0" max="1000"
183-
label="Minimum score of EPM" />
184-
185-
<param argument="--inexact-struct-match" type="boolean"
186-
truevalue="--inexact-struct-match" falsevalue=""
187-
label="Allow inexact structure matches"/>
188-
189-
<param argument="--add-filter" type="boolean"
190-
truevalue="--add-filter" falsevalue="" checked="false"
191-
label="Apply an additional filter to enumerate only
192-
EPMs that are maximally extended (only inexact)"/>
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<param argument="--no-chaining" type="boolean"
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truevalue="" falsevalue="--no-chaining" checked="true"
196-
label="Find best overall chain by chaining"/>
197-
198-
<param argument="--out-min-prob"
199-
type="float" value="0.0005" min="0" max="1"
200-
label="Minimal probability in output (min-prob overrides if smaller)"/>
201-
131+
<param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
132+
<param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
133+
<param argument="--add-filter" type="boolean" truevalue="--add-filter" falsevalue="" checked="false" label="Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)"/>
134+
<param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
135+
<param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
202136
</section>
203137
</inputs>
204138

205139
<outputs>
206140
<expand macro="standard_outupt" />
207-
<data format="ps" name="ps_fileA"
208-
label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
141+
<data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
209142
<filter>'postscript' in outputs</filter>
210143
</data>
211-
<data format="ps" name="ps_fileB"
212-
label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
144+
<data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
213145
<filter>'postscript' in outputs</filter>
214146
</data>
215-
<data format="txt" name="anchors_fasta"
216-
label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
147+
<data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
217148
<filter>'anchors-fasta' in outputs</filter>
218149
</data>
219-
<data format="txt" name="anchors_ppA"
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label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
150+
<data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
221151
<filter>'anchors-pp' in outputs</filter>
222152
</data>
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<data format="txt" name="anchors_ppB"
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label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
153+
<data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
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<filter>'anchors-pp' in outputs</filter>
226155
</data>
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<data format="clustal" name="clustal"
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label="${tool.name} on ${on_string}: chain as alignment (clustal)">
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<data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
229157
<filter>'clustal' in outputs</filter>
230158
</data>
231-
<data format="tabular" name="epm_list"
232-
label="${tool.name} on ${on_string}: list of epms">
159+
<data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">
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<filter>'epm_list' in outputs</filter>
234161
</data>
235-
<data format="tabular" name="chained_epm_list"
236-
label="${tool.name} on ${on_string}: list of epms in chain">
162+
<data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
237163
<filter>'chained_epm_list' in outputs</filter>
238164
</data>
239165
</outputs>
240166

241167
<tests>
242168
<test expect_num_outputs="2">
243-
<param name="inputA" value="tRNA_2-1.fa" />
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<param name="inputB" value="tRNA_2-2.fa" />
245-
<param name="outputs" value="epm_list" />
246-
<output name="epm_list" file="tRNA_2.epms" />
169+
<param name="inputA" value="tRNA_2-1.fa"/>
170+
<param name="inputB" value="tRNA_2-2.fa"/>
171+
<param name="outputs" value="epm_list"/>
172+
<output name="epm_list" file="tRNA_2.epms"/>
247173
<output name="stdout">
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<assert_contents>
249175
<has_text text="LCSEPM preprocessing..."/>

‎tools/rna_tools/locarna/locarna_multiple.xml‎

Lines changed: 10 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -2,20 +2,14 @@
22
<description>
33
Multiple Alignment and Folding of RNAs (mlocarna)
44
</description>
5-
65
<macros>
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<import>macros.xml</import>
87
</macros>
9-
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<expand macro="requirements" />
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<expand macro="stdio" />
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<expand macro="requirements"/>
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<expand macro="stdio"/>
1410
<expand macro="version" />
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<command><![CDATA[
1712
mlocarna
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'$input_data'
2014
#if 'stockholm' in str($outputs).split(","):
2115
--stockholm
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2519
## maybe reenable later? see https://github.com/s-will/LocARNA/issues/77
2620
## --width 60
2721
28-
## -------------------- alignment mode and specific options
29-
#
22+
## -------------------- alignment mode and specific option--------- #
3023
#if str($alignment_mode.alignment_mode_selector) == "global_locarna"
3124
$alignment_mode.free_endgaps
3225
#elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
@@ -78,30 +71,21 @@
7871
<option value="text">Fasta-like input with LocARNA constraints</option>
7972
</param>
8073
<when value="fasta">
81-
<param name="input_data" type="data" format="fasta" label="Sequence input"
82-
help="Sequence input in pure fasta format"
83-
/>
74+
<param name="input_data" type="data" format="fasta" label="Sequence input" help="Sequence input in pure fasta format"/>
8475
</when>
8576
<when value="text">
86-
<param name="input_data" type="data" format="text" label="Sequence input"
87-
help="Sequence input in fasta format with locarna-specific extensions"
88-
/>
77+
<param name="input_data" type="data" format="text" label="Sequence input" help="Sequence input in fasta format with locarna-specific extensions"/>
8978
</when>
9079
</conditional>
9180
<conditional name="alignment_mode">
92-
<param name="alignment_mode_selector" type="select" label="Alignment mode"
93-
help="Note that local alignment mode usually requires to turn off
94-
the 'max-diff' heuristic (maximal difference for alignment traces)."
95-
>
81+
<param name="alignment_mode_selector" type="select" label="Alignment mode" help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces).">
9682
<option value="global_locarna">Global alignment (LocARNA)</option>
9783
<option value="local_locarna">Local alignment (LocARNA)</option>
9884
<option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
9985
<option value="sparse">Global fast alignment (SPARSE)</option>
10086
</param>
10187
<when value="global_locarna">
102-
<param name="free_endgaps" type="select" label="Free endgaps"
103-
help="Specify whether gaps at the ends (all, 5', or 3' ends)
104-
of the sequences should be penalized or allowed for free.">
88+
<param name="free_endgaps" type="select" label="Free endgaps" help="Specify whether gaps at the ends (all, 5', or 3' ends)of the sequences should be penalized or allowed for free.">
10589
<option value="">No free endgaps</option>
10690
<option value="--free-endgaps">Free endgaps</option>
10791
<option value="--free-endgaps-5">Free endgaps, only 5'</option>
@@ -111,17 +95,9 @@
11195
<when value="local_locarna">
11296
</when>
11397
<when value="probabilistic">
114-
<param name="consistency_transformation" type="boolean"
115-
truevalue="--consistency-transformation" falsevalue=""
116-
checked="true" label="Consistency transformation"
117-
help="--consistency-transformation" />
118-
<param name="iterate" type="boolean"
119-
truevalue="true" falsevalue="false"
120-
checked="false" label="Iterative refinement"
121-
help="--iterate" />
122-
<param name="iterations" type="integer"
123-
value="1" label="Number of refinement iterations"
124-
help="--iterations num" />
98+
<param name="consistency_transformation" type="boolean" truevalue="--consistency-transformation" falsevalue="" checked="true" label="Consistency transformation" help="--consistency-transformation"/>
99+
<param name="iterate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Iterative refinement" help="--iterate"/>
100+
<param name="iterations" type="integer" value="1" label="Number of refinement iterations" help="--iterations num"/>
125101
</when>
126102
<when value="sparse">
127103
<section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">

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