| Previous changeset 2:edc663aadfa8 (2017-11-17) Next changeset 4:de387b2b2803 (2019-02-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit aaac63680661511b90969309434043ce946d6501 |
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modified:
megahit_wrapper.xml |
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removed:
test-data/single_result.fa |
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| diff -r edc663aadfa8 -r 98242353faa4 megahit_wrapper.xml --- a/megahit_wrapper.xml Fri Nov 17 08:10:37 2017 -0500 +++ b/megahit_wrapper.xml Mon May 14 06:11:34 2018 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool id="megahit" name="MEGAHIT" version="@VERSION@.2"> +<tool id="megahit" name="MEGAHIT" version="@VERSION@.3"> <description>for metagenomics assembly</description> <macros> <token name="@VERSION@">1.1.2</token> @@ -14,8 +14,14 @@ -1 '${input_option.fastq_input1}' -2 '${input_option.fastq_input2}' #else if $input_option.choice == 'paired_collection' - -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) } - -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) } + + #if $input_option.batchmode.processmode == 'merge': + -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.batchmode.pair_input_list]) } + -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.batchmode.pair_input_list]) } + #else: + -1 '${input_option.batchmode.pair_input.forward}' + -2 '${input_option.batchmode.pair_input.reverse}' + #end if #else -r '${input_option.single_files}' #end if @@ -51,7 +57,18 @@ <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/> </when> <when value="paired_collection"> - <param name="fastq_input1" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="list:paired" label="Select a paired collection"/> + <conditional name="batchmode"> + <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one assembly dataset for each fastq pair-end dataset. Selecting the merge option will produce one assembly dataset for all input fastq pair-end datasets" display="radio"> + <option value="individual" selected="true">Run individually</option> + <option value="merge">Merge all fastq pair-end</option> + </param> + <when value="individual"> + <param name="pair_input" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="paired" label="Select a paired collection"/> + </when> + <when value="merge"> + <param name="pair_input_list" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="list:paired" label="Select a paired collection"/> + </when> + </conditional> </when> </conditional> <section name="basic_section" title="Basic assembly options" expanded="True"> @@ -81,7 +98,11 @@ <param name="choice" value="single"/> <param name="single_files" value="refExample.fa" ftype="fasta"/> </conditional> - <output name="output" file="single_result.fa"/> + <output name="output"> + <assert_contents> + <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" /> + </assert_contents> + </output> </test> <test> <conditional name="input_option"> @@ -92,20 +113,23 @@ <output name="output" file="paired_result.fa"/> </test> <test> - <conditional name="input_option"> - <param name="choice" value="paired_collection"/> - <param name="fastq_input1"> - <collection type="list:paired"> - <element name="Pair1"> - <collection type="paired"> - <element name="forward" value="paired-fq1.fa" ftype="fasta"/> - <element name="reverse" value="paired-fq2.fa" ftype="fasta"/> - </collection> - </element> - </collection> - </param> + <conditional name="input_option"> + <param name="choice" value="paired_collection"/> + <conditional name="batchmode"> + <param name="processmode" value="merge"/> + <param name="pair_input_list"> + <collection type="list:paired"> + <element name="Pair1"> + <collection type="paired"> + <element name="forward" value="paired-fq1.fa" ftype="fasta"/> + <element name="reverse" value="paired-fq2.fa" ftype="fasta"/> + </collection> + </element> + </collection> + </param> </conditional> - <output name="output" file="paired_result.fa"/> + </conditional> + <output name="output" file="paired_result.fa"/> </test> </tests> <help><![CDATA[ |
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| diff -r edc663aadfa8 -r 98242353faa4 test-data/single_result.fa --- a/test-data/single_result.fa Fri Nov 17 08:10:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ ->k21_1 flag=3 multi=1.0486 len=576 -GGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAAC |