comparison chira_extract.xml @ 18:e7ee3aadf1a5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 28963347255f1df6efaa8991ad9fc17f86b30a73"

17:8b2c1d1556ac

<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
    <description>extrat the chimeras</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        #set $genomic_fasta = ''
        #if str($annotation.annot_choice) == "yes":
            #if str($annotation.fasta_source.fasta_source_selector) == 'history':
                #set $genomic_fasta = $annotation.fasta_source.fasta
            #else
                #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
            #end if
        #end if
        chira_extract.py

18:e7ee3aadf1a5

<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
    <description>extrat the chimeras</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        #set $genomic_fasta = ''
        #if str($annotation.annot_choice) == "yes":
            #if str($annotation.fasta_source.fasta_source_selector) == 'history':
                ## Avoid writing FASTA index to inputdir by symlinking 
                ln -s '${$annotation.fasta_source.fasta}' genome.fa &&
                #set $genomic_fasta = 'genome.fa'
            #else
                #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
            #end if
        #end if
        chira_extract.py