Mercurial > repos > iuc > seq2hla
diff seq2hla.xml @ 2:86d0ce0560a1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
| author | iuc |
|---|---|
| date | Tue, 07 Mar 2023 13:10:18 +0000 |
| parents | 5a7cd6c39085 |
| children |
line wrap: on
line diff
--- a/seq2hla.xml Wed Apr 07 12:37:40 2021 +0000 +++ b/seq2hla.xml Tue Mar 07 13:10:18 2023 +0000 @@ -1,19 +1,31 @@ -<tool id="seq2hla" name="seq2HLA" version="2.2.0+galaxy1"> +<tool id="seq2hla" name="seq2HLA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>HLA genotype and expression from RNA-seq</description> + <macros> + <token name="@TOOL_VERSION@">2.3</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">seq2hla</xref> + </xrefs> <requirements> - <!-- needed because of some non POSIX compliant wc usage --> - <requirement type="package" version="8.31">coreutils</requirement> - <requirement type="package" version="2.2">seq2hla</requirement> + <requirement type="package" version="@TOOL_VERSION@">seq2hla</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - seq2HLA --runName='$run_name' -1 '$fastq_input1' -2 '$fastq_input2' + seq2HLA --runName='$run_name' + #if str( $fastq_input.fastq_input_selector ) == "paired": + -1 '${fastq_input.fastq_input1}' + -2 '${fastq_input.fastq_input2}' + #elif str( $fastq_input.fastq_input_selector ) == "paired_collection": + -1 '${fastq_input.fastq_input1.forward}' + -2 '${fastq_input.fastq_input1.reverse}' + #end if #if str($trim) != '': --trim3=$trim #end if -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log' - && cp -p '${run_name}-ClassI.HLAgenotype2digits' '${c1_genotype2digits}' - && cp -p '${run_name}-ClassI.HLAgenotype4digits' '${c1_genotype4digits}' - && echo '#Locus_RPKM' | cat - '${run_name}-ClassI.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}' + && cp -p '${run_name}-ClassI-class.HLAgenotype2digits' '${c1_genotype2digits}' + && cp -p '${run_name}-ClassI-class.HLAgenotype4digits' '${c1_genotype4digits}' + && echo '#Locus_RPKM' | cat - '${run_name}-ClassI-class.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}' && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}' && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}' && cp -p '${run_name}.ambiguity' '${ambiguity}' @@ -22,8 +34,19 @@ <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis"> <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator> </param> - <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Paired-end reads" help="Select between paired and paired-collection data"> + <option value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a collection of paired-end reads"/> + </when> + </conditional> <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" help="trim this many bases from the low-quality end of each read" /> </inputs> @@ -34,14 +57,33 @@ <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/> <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/> <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/> - <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/> <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/> </outputs> <tests> <test> <param name="run_name" value="test"/> - <param name="fastq_input1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/> - <param name="fastq_input2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/> + <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/> + </conditional> + <output name="c1_genotype4digits"> + <assert_contents> + <has_text text="A*24:02" /> + </assert_contents> + </output> + </test> + <test> + <param name="run_name" value="test_collection"/> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired_collection"/> + <param name="fastq_input1"> + <collection type="paired"> + <element name="forward" ftype="fastqsanger" value="reads1.fastq" /> + <element name="reverse" ftype="fastqsanger" value="reads2.fastq" /> + </collection> + </param> + </conditional> <output name="c1_genotype4digits"> <assert_contents> <has_text text="A*24:02" /> @@ -97,7 +139,7 @@ ======= ====== -.. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla +.. _seq2HLA: https://github.com/TRON-Bioinformatics/seq2HLA ]]></help> <citations>