comparison cuffmerge_wrapper.xml @ 12:1707a530e598 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

11:8160c8ea4eb9

<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
    <description>merge together several Cufflinks assemblies</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <command interpreter="python">
        cuffmerge_wrapper.py
            --num-threads="\${GALAXY_SLOTS:-4}"
            
            ## Use annotation reference?
            #if $annotation.use_ref_annotation == "Yes":
                -g "${annotation.reference_annotation}"
            #end if
            
            ## Use sequence data?
            #if $seq_data.use_seq_data == "Yes":
                -s
                #if $seq_data.seq_source.index_source == "history":
                    --ref_file="${seq_data.seq_source.ref_file}"
                #else:
                    --index="${seq_data.seq_source.index.fields.path}"
                #end if
            #end if

            --min-isoform-fraction="${min_isoform_fraction}"

            ## Outputs.
            --merged-transcripts="${merged_transcripts}"

            @CUFFLINKS_GTF_INPUTS@
    </command>
    <inputs>
        <expand macro="cufflinks_gtf_inputs" />

12:1707a530e598

<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
    <description>merge together several Cufflinks assemblies</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        python '$__tool_directory__/cuffmerge_wrapper.py'
            --num-threads="\${GALAXY_SLOTS:-4}"
            
            ## Use annotation reference?
            #if $annotation.use_ref_annotation == "Yes":
                -g '${annotation.reference_annotation}'
            #end if
            
            ## Use sequence data?
            #if $seq_data.use_seq_data == "Yes":
                -s
                #if $seq_data.seq_source.index_source == "history":
                    --ref_file '${seq_data.seq_source.ref_file}'
                #else:
                    --index '${seq_data.seq_source.index.fields.path}'
                #end if
            #end if

            --min-isoform-fraction="${min_isoform_fraction}"

            ## Outputs.
            --merged-transcripts '${merged_transcripts}'

            @CUFFLINKS_GTF_INPUTS@
    </command>
    <inputs>
        <expand macro="cufflinks_gtf_inputs" />