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dadrasarmindadrasarmin
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Modified tools to pass planemo lint and corrected one test_data
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11 files changed

+69
-39
lines changed

11 files changed

+69
-39
lines changed

‎tools/text_processing/text_processing/cut.xml‎

Lines changed: 12 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -191,14 +191,19 @@
191191
<tests>
192192
<test expect_num_outputs="1">
193193
<param name="input" value="cut1.txt"/>
194-
<param name="list" value="1,3,4"/>
195-
<param name="delimiter" value=""/>
194+
<conditional name="cut_type_options">
195+
<param name="cut_element" value="-f"/>
196+
<param name="delimiter" value="" />
197+
<conditional name="colnames_option">
198+
<param name="header" value="Y"/>
199+
<param name="list" value="1,3,4"/>
200+
</conditional>
201+
</conditional>
196202
<output name="output" file="cut_results1.txt"/>
197203
<assert_command>
198204
<has_text text="-f '1,3,4'"/>
199205
</assert_command>
200206
</test>
201-
202207
<test expect_num_outputs="1">
203208
<param name="input" value="cut1.txt"/>
204209
<conditional name="cut_type_options">
@@ -217,9 +222,10 @@
217222
</test>
218223
<test expect_num_outputs="1">
219224
<param name="input" value="cut1.txt"/>
220-
<param name="list" value="-3" />
221-
<param name="delimiter" value="" />
222-
<param name="cut_element" value="-c" />
225+
<conditional name="cut_type_options">
226+
<param name="cut_element" value="-c" />
227+
<param name="list" value="-3" />
228+
</conditional>
223229
<output name="output" file="cut_results3.txt"/>
224230
</test>
225231
</tests>

‎tools/text_processing/text_processing/grep.xml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -85,7 +85,7 @@
8585
<!-- grep a FASTA file for sequences with specific motif -->
8686
<test>
8787
<param name="infile" value="grep1.txt" />
88-
<param name="case_sensitive" value="case sensitive" />
88+
<param name="case_sensitive" value="-i" />
8989
<param name="regex_type" value="-P" />
9090
<param name="invert" value="" />
9191
<param name="url_paste" value="AA.{2}GT" />
@@ -98,7 +98,7 @@
9898
show highlighed output -->
9999
<test>
100100
<param name="infile" value="grep1.txt" />
101-
<param name="case_sensitive" value="case sensitive" />
101+
<param name="case_sensitive" value="-i" />
102102
<param name="regex_type" value="-P" />
103103
<param name="invert" value="" />
104104
<param name="url_paste" value="AA.{2}GT" />
@@ -110,7 +110,7 @@
110110
<!-- tests egrep -->
111111
<test>
112112
<param name="infile" value="egrep1.txt" />
113-
<param name="case_sensitive" value="case sensitive" />
113+
<param name="case_sensitive" value="-i" />
114114
<param name="regex_type" value="-E" />
115115
<param name="invert" value="" />
116116
<param name="url_paste" value="[^ ]+" />
@@ -122,7 +122,7 @@
122122
<!-- tests basic regex; + must be backslashed to match -->
123123
<test>
124124
<param name="infile" value="egrep1.txt" />
125-
<param name="case_sensitive" value="case sensitive" />
125+
<param name="case_sensitive" value="-i" />
126126
<param name="regex_type" value="-G" />
127127
<param name="invert" value="" />
128128
<param name="url_paste" value="[^ ]\+" />
@@ -134,7 +134,7 @@
134134
<!-- tests regex;matching nothing -->
135135
<test>
136136
<param name="infile" value="egrep1.txt" />
137-
<param name="case_sensitive" value="case sensitive" />
137+
<param name="case_sensitive" value="-i" />
138138
<param name="regex_type" value="-G" />
139139
<param name="invert" value="" />
140140
<param name="url_paste" value="not existent pattern" />
@@ -150,7 +150,7 @@
150150
<!-- tests invalid regex; i.e. that we still get exit code 2 -->
151151
<test expect_failure="true" expect_exit_code="2">
152152
<param name="infile" value="egrep1.txt" />
153-
<param name="case_sensitive" value="case sensitive" />
153+
<param name="case_sensitive" value="-i" />
154154
<param name="regex_type" value="-G" />
155155
<param name="invert" value="" />
156156
<param name="url_paste" value="\(" />

‎tools/text_processing/text_processing/multijoin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,7 @@
5252
<param name="first_file" value="multijoin1.txt" />
5353
<param name="files" value="multijoin2.txt,multijoin3.txt" />
5454
<param name="key_column" value="4" />
55-
<param name="value_columns" value="c7,c8,c9" />
55+
<param name="value_columns" value="7,8,9" />
5656
<param name="output_header" value="True" />
5757
<output name="outfile" file="multijoin_result1.txt" lines_diff="2" />
5858
</test>

‎tools/text_processing/text_processing/recurring_lines.xml‎

Lines changed: 12 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -44,21 +44,27 @@
4444
<test>
4545
<repeat name="token_set">
4646
<param name="line" value="freedom" />
47-
<param name="repeat_select_opts" value="file" />
48-
<param name="infile" value="multijoin2.txt" />
47+
<conditional name="repeat_select">
48+
<param name="repeat_select_opts" value="file" />
49+
<param name="infile" value="multijoin2.txt" />
50+
</conditional>
4951
</repeat>
5052
<output name="outfile" file="recurring_result1.txt" />
5153
</test>
5254
<test>
5355
<repeat name="token_set">
5456
<param name="line" value="freedom" />
55-
<param name="repeat_select_opts" value="user" />
56-
<param name="times" value="10" />
57+
<conditional name="repeat_select">
58+
<param name="repeat_select_opts" value="user" />
59+
<param name="times" value="10" />
60+
</conditional>
5761
</repeat>
5862
<repeat name="token_set">
5963
<param name="line" value="war is over" />
60-
<param name="repeat_select_opts" value="user" />
61-
<param name="times" value="10" />
64+
<conditional name="repeat_select">
65+
<param name="repeat_select_opts" value="user" />
66+
<param name="times" value="10" />
67+
</conditional>
6268
</repeat>
6369
<output name="outfile" file="recurring_result2.txt" />
6470
</test>

‎tools/text_processing/text_processing/replace_text_in_column.xml‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -51,9 +51,11 @@
5151
<tests>
5252
<test>
5353
<param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
54-
<param name="column" value="4" />
55-
<param name="find_pattern" value=".+_(R.)" />
56-
<param name="replace_pattern" value="\\1" />
54+
<repeat name="replacements">
55+
<param name="column" value="4" />
56+
<param name="find_pattern" value=".+_(R.)" />
57+
<param name="replace_pattern" value="\\1" />
58+
</repeat>
5759
<output name="outfile" file="replace_text_in_column_results1.txt" />
5860
</test>
5961
<test>

‎tools/text_processing/text_processing/replace_text_in_line.xml‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -70,9 +70,11 @@
7070
<tests>
7171
<test>
7272
<param name="infile" value="replace_text_in_line1.txt" />
73-
<param name="find_pattern" value="CTC." />
74-
<param name="replace_pattern" value="FOOBAR" />
75-
<param name="sed_options" value="" />
73+
<repeat name="replacements">
74+
<param name="find_pattern" value="CTC." />
75+
<param name="replace_pattern" value="FOOBAR" />
76+
<param name="sed_options" value="" />
77+
</repeat>
7678
<output name="outfile" file="replace_text_in_line_results1.txt" />
7779
</test>
7880
<test>
@@ -91,9 +93,11 @@
9193
</test>
9294
<test>
9395
<param name="infile" value="replace_text_in_line1.txt" />
96+
<repeat name="replacements">
9497
<param name="find_pattern" value="\n" />
9598
<param name="replace_pattern" value="" />
9699
<param name="sed_options" value=":a;N;$!ba" />
100+
</repeat>
97101
<output name="outfile" file="replace_text_in_line_results3.txt" />
98102
</test>
99103
</tests>

‎tools/text_processing/text_processing/sed.xml‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -56,14 +56,19 @@
5656
<test>
5757
<param name="infile" value="sed1.txt" />
5858
<param name="code" value="1d ; s/foo/bar/" />
59-
<param name="silent" value="" />
59+
<conditional name="adv_opts">
60+
<param name="adv_opts_selector" value="advanced" />
61+
<param name="silent" value="" />
62+
</conditional>
6063
<output name="output" file="sed_results1.txt" />
6164
</test>
6265
<test>
6366
<param name="infile" value="sed1.txt" />
6467
<param name="code" value="/foo/ { s/foo/baz/g ; p }" />
65-
<param name="adv_opts_selector" value="advanced" />
66-
<param name="silent" value="-n" />
68+
<conditional name="adv_opts">
69+
<param name="adv_opts_selector" value="advanced" />
70+
<param name="silent" value="-n" />
71+
</conditional>
6772
<output name="output" file="sed_results2.txt" />
6873
</test>
6974
</tests>

‎tools/text_processing/text_processing/sorted_uniq.xml‎

Lines changed: 9 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -74,17 +74,21 @@
7474
<tests>
7575
<test>
7676
<param name="infile" value="sorted_uniq1.tabular" />
77-
<param name="grouping_select" value="no"/>
78-
<param name="count" value="True"/>
77+
<conditional name="grouping">
78+
<param name="grouping_select" value="no"/>
79+
<param name="count" value="True"/>
80+
<param name="uniqueonly" value="True"/>
81+
</conditional>
7982
<param name="ignorecase" value="True"/>
80-
<param name="uniqueonly" value="True"/>
8183
<output name="outfile" file="sorted_uniq_results1.tabular" />
8284
</test>
8385
<test>
8486
<param name="infile" value="sorted_uniq1.tabular" />
8587
<param name="ignorecase" value="True"/>
86-
<param name="grouping_select" value="yes"/>
87-
<param name="group" value="separate"/>
88+
<conditional name="grouping">
89+
<param name="grouping_select" value="yes"/>
90+
<param name="group" value="separate"/>
91+
</conditional>
8892
<output name="outfile" file="sorted_uniq_results2.tabular" />
8993
</test>
9094
</tests>

‎tools/text_processing/text_processing/tac.xml‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,10 @@
4848
</test>
4949
<test>
5050
<param name="infile" value="1.bed"/>
51-
<param name="separator_select" value="yes"/>
52-
<param name="before" value="True"/>
51+
<conditional name="separator">
52+
<param name="separator_select" value="yes"/>
53+
<param name="before" value="True"/>
54+
</conditional>
5355
<output name="outfile" file="tac_result2.txt"/>
5456
</test>
5557
</tests>

‎tools/text_processing/text_processing/test-data/recurring_result1.txt‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,4 +7,3 @@ freedom
77
freedom
88
freedom
99
freedom
10-
freedom

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