Mercurial > repos > public-health-bioinformatics > micall_lite
diff micall_lite.xml @ 0:023064145bea draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
| author | public-health-bioinformatics |
|---|---|
| date | Mon, 06 Jan 2020 19:10:15 -0500 |
| parents | |
| children | bb549c5eaf34 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/micall_lite.xml Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,148 @@ +<tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement> + </requirements> + <version_command>echo "@TOOL_VERSION@"</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #if str( $fastq_input.fastq_input_selector ) == "paired": + #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz' + #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq' + #end if + ln -s '$fastq_input.reads1' '$reads1' && + #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz' + #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq' + #end if + ln -s '$fastq_input.reads2' '$reads2' && + #else if str( $fastq_input.fastq_input_selector ) == "paired_collection": + #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz' + #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq' + #end if + ln -s '$fastq_input.pair.forward' '$reads1' && + #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz' + #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq' + #end if + ln -s '$fastq_input.pair.reverse' '$reads2' && + #end if + + mkdir 'outdir' && + micall + --threads \${GALAXY_SLOTS:-1} + #if $unzipped: + --unzipped + #end if + --readlen ${readlen} + '${reads1}' + '${reads2}' + --outdir 'outdir' + ]]> + </command> + <inputs> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" > + <option selected="true" value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/> + <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/> + </when> + <when value="paired_collection"> + <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/> + </when> + </conditional> + <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" /> + </inputs> + <outputs> + <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" /> + <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" /> + <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" /> + <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" /> + <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" /> + </outputs> + <tests> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> + <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" /> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> + <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" /> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired_collection" /> + <param name="pair" > + <collection type="paired"> + <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> + <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" /> + </collection> + </param> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired_collection" /> + <param name="pair" > + <collection type="paired"> + <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> + <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" /> + </collection> + </param> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <expand macro="citations" /> +</tool>