Mercurial > repos > iuc > semibin_concatenate_fasta
view concatenate_fasta.xml @ 2:298542e0e136 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
author | iuc |
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date | Fri, 10 Nov 2023 20:50:29 +0000 |
parents | e6bc3455940e |
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<tool id="semibin_concatenate_fasta" name="SemiBin: Concatenate fasta files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> for multi-sample binning </description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #import re #for $e in $input_fasta #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) #if $e.ext.endswith(".gz") gunzip -c '$e' > '${identifier}.fasta' && #else ln -s '$e' '${identifier}.fasta' && #end if #end for SemiBin2 concatenate_fasta --input-fasta *.fasta --output 'output' --separator '$separator' --compression none -m $min_len ]]></command> <inputs> <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/> <expand macro="separator"/> <expand macro="concat_min_len"/> </inputs> <outputs> <data name="fasta" format="fasta" from_work_dir="output/concatenated.fa" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/> <param name="separator" value=":"/> <param name="min_len" value="0"/> <output name="fasta" ftype="fasta"> <assert_contents> <has_text text=">input_single:g1k_0"/> <has_text text=">input_single_3:g4k_7"/> <has_text text=">input_single_2:g1k_0"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Inputs ====== @HELP_INPUT_FASTA@ Outputs ======= - One fasta with all contigs ]]></help> <expand macro="citations"/> </tool>