annotate macros.xml @ 0:f78303e25f3e draft

"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"

<macros>
    <token name="@TOOL_VERSION@">1.8.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">ipa_hifi</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
	   <requirements>
        	<requirement type="package" version="@TOOL_VERSION@">pbipa</requirement>
           </requirements>
   </xml>
   <xml name="stdio">
     <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
   <token name="@CONDA_IPA_PATH@">if [ -z "\$IPA_PATH" ]; then export IPA_PATH=\$(dirname \$(dirname \$(readlink -e \$(which ipa)))); fi</token>
   <xml name="version_command">
      <version_command><![CDATA[
       if [ -z "$IPA_PATH" ]; then export IPA_PATH=$(dirname $(dirname $(readlink -e $(which ipa)))); fi &&
	      "$IPA_PATH/bin/ipa" --version 2>&1 | head -1       
      ]]></version_command>
  </xml>
  <xml name="macro_input">
       <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file"/>
  </xml>
  <token name="@PREPARE_INPUT_FILE@">
     <![CDATA[
     #set $pacbio_input_file = 'input.fastq'
     #if $input_file.is_of_type('fastq')
         cp '$input_file' $pacbio_input_file
     #elif $input_file.is_of_type('fasta')
         #set $pacbio_input_file = 'input.fasta'
	 cp '$input_file' $pacbio_input_file
     #elif $input_file.is_of_type('bam')		  
         #set $pacbio_input_file = 'input.bam'		  
         cp '$input_file' $pacbio_input_file 
     #end if
     ]]>
  </token>
  <token name="@INPUT_FILE@">
        $pacbio_input_file
  </token>   
  <xml name="macro_inputs">
      <param name="input_files" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file datasets" multiple="True" />
  </xml>
  <token name="@PREPARE_INPUT_FILES@">
     <![CDATA[
      #set $pacbio_input_files = []
      #set $pacbio_list_file = 'pacbio_list'
      #for (i, input_file) in enumerate($input_files):
  	#set $pacbio_input_file = 'input' + str($i) + '.fastq'
  	#if $pacbio_input_file.is_of_type('fastq')
    	    cp '$input_file' $pacbio_input_file
        #elif $input_file.is_of_type('fasta')
	    #set $pacbio_input_file = 'input' + str($i) + 'fasta'
            cp '$input_file' $pacbio_input_file
  	#elif $input_file.is_of_type('bam')
	    #set $pacbio_input_file = 'input' + str($i) + 'bam'
            cp '$input_file' $pacbio_input_file
  	#end if
  	echo '$pacbio_input_file' >> $pacbio_list_file &&
  	$pacbio_input_files.append($pacbio_input_file)
      #end for
     ]]>
  </token>
    <token name="@INPUT_FILES@">
	#echo ' '.join($pacbio_input_files)#
  </token>
  <token name="@INPUT_LIST_FILE@">
	$pacbio_list_file
  </token>
</macros>