| Previous changeset 1:269da71211ff (2017-09-27) Next changeset 3:98242353faa4 (2018-05-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c |
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modified:
megahit_wrapper.xml |
| b |
| diff -r 269da71211ff -r edc663aadfa8 megahit_wrapper.xml --- a/megahit_wrapper.xml Wed Sep 27 05:31:34 2017 -0400 +++ b/megahit_wrapper.xml Fri Nov 17 08:10:37 2017 -0500 |
| [ |
| @@ -1,28 +1,30 @@ <?xml version='1.0' encoding='utf-8'?> -<tool id="megahit" name="MEGAHIT" version="1.1.2.1"> - <description>metagenomics assembly</description> +<tool id="megahit" name="MEGAHIT" version="@VERSION@.2"> + <description>for metagenomics assembly</description> + <macros> + <token name="@VERSION@">1.1.2</token> + </macros> <requirements> - <requirement type="package" version="1.1.2">megahit</requirement> + <requirement type="package" version="@VERSION@">megahit</requirement> </requirements> <version_command>megahit --version</version_command> <command detect_errors="exit_code"><![CDATA[ - - megahit - +megahit #if $input_option.choice == 'paired' + -1 '${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 $input_option.fastq_input1]) } #else -r '${input_option.single_files}' #end if - ##basic assembly --min-count '${basic_section.min_count}' --k-min '${basic_section.k_min}' --k-max '${basic_section.k_max}' --k-step '${basic_section.k_step}' --min-contig-len '${basic_section.min_contig_len}' - ##advanced assembly ${advanced_section.nomercy} --bubble-level '${advanced_section.bubble_level}' @@ -32,24 +34,24 @@ --low-local-ratio '${advanced_section.low_local_ratio}' ${advanced_section.nolocal} ${advanced_section.kmin1pass} - - && - - cat megahit_out/log - +&& cat megahit_out/log ]]></command> - <inputs> <conditional name="input_option"> <param name="choice" type="select" label="Select your input option"> <option value="single" selected="true">Single</option> <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end collection</option> </param> + <when value="single"> + <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" /> + </when> <when value="paired"> - <param name="fastq_input1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="list:paired" label="Select a paired collection"/> + <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/> + <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="single"> - <param name="single_files" multiple="true" format="fastq,fastqsanger,fasta" type="data" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" /> + <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"/> </when> </conditional> <section name="basic_section" title="Basic assembly options" expanded="True"> @@ -84,6 +86,14 @@ <test> <conditional name="input_option"> <param name="choice" value="paired"/> + <param name="fastq_input1" value="paired-fq1.fa"/> + <param name="fastq_input2" value="paired-fq2.fa"/> + </conditional> + <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"> @@ -98,7 +108,6 @@ <output name="output" file="paired_result.fa"/> </test> </tests> - <help><![CDATA[ **What it does** |