Mercurial > repos > iuc > disco
changeset 2:dfefaf2bab95 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
| author | iuc |
|---|---|
| date | Sun, 18 Apr 2021 17:48:28 +0000 |
| parents | 6de3e77073ad |
| children | |
| files | disco.xml test-data/ecoli_1K_1.fq.gz test-data/ecoli_1K_2.fq.gz |
| diffstat | 3 files changed, 53 insertions(+), 18 deletions(-) [+] |
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--- a/disco.xml Wed May 02 05:47:09 2018 -0400 +++ b/disco.xml Sun Apr 18 17:48:28 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.0"> +<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01"> <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description> <macros> <token name="@WRAPPER_VERSION@">1.2</token> @@ -20,21 +20,55 @@ <requirements> <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement> </requirements> - <version_command>runDisco.sh --version</version_command> + <version_command>echo @WRAPPER_VERSION@</version_command> <command detect_errors="exit_code"><![CDATA[ +#if $input_cond.library_type == "single" + #for i, e in enumerate($input_cond.inS) + cp '$e' + #if $e.ext.endswith(".gz") + input_${i}.fastq.gz && + #else + input_${i}.fastq && + #end if + #end for +#else + #if $input_cond.paired_input.type == "separated" + #if $input_cond.paired_input.in1.ext.endswith(".gz") + cp '$input_cond.paired_input.in1' forward.fastq.gz && + cp '$input_cond.paired_input.in2' reverse.fastq.gz && + #else + cp '$input_cond.paired_input.in1' forward.fastq && + cp '$input_cond.paired_input.in2' reverse.fastq && + #end if + #else + #for i, e in enumerate($input_cond.paired_input.inP) + cp '$e' + #if $e.ext.endswith(".gz") + input_${i}.fastq.gz && + #else + input_${i}.fastq && + #end if + #end for + #end if +#end if runDisco.sh -n \${GALAXY_SLOTS:-4} -m \${DISCO_MAX_MEMORY:-4} -d . -o disco - #if $input.library_type == "single" - -inS '$input.inS' + #if $input_cond.library_type == "single" + -inS \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//') #else - #if $input.paired_input.type == "separated" - -in1 '$input.paired_input.in1' - -in2 '$input.paired_input.in2' + #if $input_cond.paired_input.type == "separated" + #if $input_cond.paired_input.in1.ext.endswith(".gz") + -in1 forward.fastq.gz + -in2 reverse.fastq.gz + #else + -in1 forward.fastq + -in2 reverse.fastq + #end if #else - -inP '$input.paired_input.inP' + -inP \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//') #end if #end if $obg @@ -109,13 +143,13 @@ ]]></configfile> </configfiles> <inputs> - <conditional name="input"> + <conditional name="input_cond"> <param name="library_type" type="select" label="Type of library?"> <option value="single">Single-end reads</option> <option value="paired">Paired-end reads</option> </param> <when value="single"> - <param argument="-inS" type="data" format="fastq,fasta" multiple="true" label="Single-read files"/> + <param argument="-inS" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Single-read files"/> </when> <when value="paired"> <conditional name="paired_input"> @@ -124,11 +158,11 @@ <option value="interleaved">Interleaved paired-read files</option> </param> <when value="separated"> - <param argument="-in1" type="data" format="fastq,fasta" label="Forward read file" /> - <param argument="-in2" type="data" format="fastq,fasta" label="Reverse read file" /> + <param argument="-in1" type="data" format="fastq,fastq.gz,fasta" label="Forward read file" /> + <param argument="-in2" type="data" format="fastq,fastq.gz,fasta" label="Reverse read file" /> </when> <when value="interleaved"> - <param argument="-inP" type="data" format="fastq,fasta" multiple="true" label="Interleaved paired-read files" /> + <param argument="-inP" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Interleaved paired-read files" /> </when> </conditional> </when> @@ -172,7 +206,7 @@ </outputs> <tests> <test> - <conditional name="input"> + <conditional name="input_cond"> <param name="library_type" value="paired"/> <conditional name="paired_input"> <param name="type" value="separated"/> @@ -265,7 +299,7 @@ </output_collection> </test> <test> - <conditional name="input"> + <conditional name="input_cond"> <param name="library_type" value="paired"/> <conditional name="paired_input"> <param name="type" value="interleaved"/> @@ -333,9 +367,9 @@ <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/> </test> <test> - <conditional name="input"> + <conditional name="input_cond"> <param name="library_type" value="single"/> - <param name="inS" value="ecoli_1K_1.fq"/> + <param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/> </conditional> <param name="obg" value=""/> <param name="osg" value=""/> @@ -393,7 +427,8 @@ <help><![CDATA[ DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach. -The detailed user manual of the assembler and how to use it to acheive best results is provided here: http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual. +The detailed user manual of the assembler and how to use it to acheive best results is provided here: + http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual. ]]></help> <citations> </citations>