add alevin-fry

tools/alevin-fry/collate.xml

@@ -0,0 +1,32 @@
+<tool id="alevin_fry_collate" name="Alevin-Fry Collate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Collate a RAD file by corrected cell barcode</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir input1 &&
+        ln -s '$input1' input1 &&
+        mkdir input2 &&
+        ln -s '$input2' input2 &&
+        alevin-fry collate --input-dir input1 --rad-dir input2
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" label="Output of 'Alevin-Fry Generate Permit List'" format="directory"/>
+        <param type="data" name="input2" label="RAD file to be collated" format="rad"/>
+    </inputs>
+    <outputs>
+        <param type="data" name="output1" label="${tool.name} on ${on_string}: $input2.collated" format="rad"/>
+        <param type="data" name="output2" label="${tool.name} on ${on_string}: collate" format="json"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- add tests -->
+        </test>
+    </tests>
+    help
+    <help>
+        help
+    </help>
+    <expand macro="citations"/>
+</tool>

tools/alevin-fry/convert.xml

@@ -0,0 +1,27 @@
+<tool id="alevin_fry_convert" name="Alevin-Fry Convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Convert BAM/SAM to RAD</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input' input.bam &&
+        alevin-fry convert --bam input.bam --output '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" label="BAM or SAM file" format="bam,sam"/>
+    </inputs>
+    <outputs>
+        <data name="output" label="${tool.name} on ${on_string}" format="rad"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="convert/input.bam"/>
+            <output name="output" file="convert/output.rad"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        help
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

tools/alevin-fry/generate-permit-list.xml

@@ -0,0 +1,52 @@
+<tool id="alevin_fry_generate_permit_list" name="Alevin-Fry Generate Permit List" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Generate a permit list of barcodes from a RAD file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir inputs &&
+        ln -s '$input' inputs/map.rad &&
+        mkdir outputs &&
+        ##ln -s '$output1' outputs &&
+        alevin-fry generate-permit-list $KNEEDISTANCE --input inputs --expected-ori '$EXPECTEDORI' --output-dir outputs
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" label="map RAD file" format="rad" help="The input file has to be called 'map.rad' for Alevin Fry to work"/>
+        <param type="select" name="EXPECTEDORI" label="Expected orientation">
+            <option value="fw">fw</option>
+            <option value="rc">rc</option>
+            <option value="both">both</option>
+            <option value="either">either</option>
+        </param>
+        <param type="boolean" name="KNEEDISTANCE" truevalue="--knee-distance" falsevalue="" label="Attempt to determine the number of barcodes to keep using the knee-distance method."/>
+        <param name="barcode_selection" type="select" label="" help="TODO">
+            <option value="knee-distance">Knee-distance method</option>
+            <option value="force-cells">TODO: force-cells</option>
+            <option value="valid-bc">TODO: valid-bc</option>
+            <option value="unfiltered-pl">TODO: unfiltered-pl</option>
+            <option value="expect-cells">TODO: expect-cells</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" label="${tool.name} on ${on_string}: all_freq" format="binary" from_work_dir="outputs/all_freq.bin"/>
+        <data name="output2" label="${tool.name} on ${on_string}: permit_freq" format="binary" from_work_dir="outputs/permit_freq.bin"/>
+        <data name="output3" label="${tool.name} on ${on_string}: permit_map" format="binary" from_work_dir="outputs/permit_map.bin"/>
+        <data name="output4" label="${tool.name} on ${on_string}: generate_permit_list" format="json" from_work_dir="outputs/generate_permit_list.json"/>
+    </outputs>
+    <tests>
+    <test expect_num_outputs="4">
+        <param name="input" value="gpltest/input"/>
+        <param name="EXPECTEDORI" value="either"/>
+        <param name="KNEEDISTANCE" value="true"/>
+        <output name="output1" file="gpltest/output/all_freq.bin"/>
+        <output name="output2" file="gpltest/output/permit_freq.bin"/>
+        <output name="output3" file="gpltest/output/permit_map.bin"/>
+        <output name="output4" file="gpltest/output/generate_permit_list.json"/>
+    </test>
+    </tests>
+    <help>
+        help
+    </help>
+    <expand macro="citations"/>
+</tool>

tools/alevin-fry/macros.xml

@@ -0,0 +1,30 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.11.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE_VERSION@">23.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">alevin-fry</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @Article{He2022,
+                    author={He, Dongze and Zakeri, Mohsen and Sarkar, Hirak and Soneson, Charlotte and Srivastava, Avi and Patro, Rob},
+                    title={Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data},
+                    journal={Nature Methods},
+                    year={2022},
+                    month={Mar},
+                    day={01},
+                    volume={19},
+                    number={3},
+                    pages={316-322},
+                    issn={1548-7105},
+                    doi={10.1038/s41592-022-01408-3},
+                    url={https://doi.org/10.1038/s41592-022-01408-3}
+                    }
+            </citation>
+        </citations>
+    </xml>
+</macros>