comparison telescope_assign.xml @ 1:2d8c943f3e8d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8

0:66ff74923224

<?xml version="1.0"?>
<tool id="telescope_assign" name="Reassign reads" version="@VERSION@">
    <description>with TELESCOPE using a statistical model</description>
    <macros>
        <token name="@VERSION@">1.0.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">telescope</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir tempdir &&
        mkdir outdir &&
        telescope assign '$input_alignment' '$input_gtf'
            --tempdir tempdir
            --outdir outdir
            --ncpu \${GALAXY_SLOTS:-1}
            $updated_sam
            #if str($advanced.advanced_options) == 'select':
                --reassign_mode $advanced.reassign_mode
                --conf_prob $advanced.conf_prob
                --overlap_mode $advanced.overlap_mode

                $advanced.use_likelihood
            #end if
        #if $updated_sam
            &&
            if [ -f outdir/telescope-updated.bam ] ; then
                samtools sort outdir/telescope-updated.bam > '$updated_alignment' ;
            else
                echo 'Updated alignment file not found.' ;
                exit 1 ;
            fi
        #end if

1:2d8c943f3e8d

<tool id="telescope_assign" name="Reassign reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>with TELESCOPE using a statistical model</description>
    <xrefs>
        <xref type="bio.tools">Telescope-expression</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">1.0.3</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">telescope</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir tempdir &&
        mkdir outdir &&
        
        telescope assign '$input_alignment' '$input_gtf'
            --tempdir tempdir
            --outdir outdir
            ## Not supported https://github.com/mlbendall/telescope/blob/6cd55256c6016feffdbfe10346bfecfcb1e30965/README.md?plain=1#L129
            ## --ncpu \${GALAXY_SLOTS:-1}
            $updated_sam
            #if str($advanced.advanced_options) == 'select':
                --reassign_mode $advanced.reassign_mode
                --conf_prob $advanced.conf_prob
                --overlap_mode $advanced.overlap_mode

                $advanced.use_likelihood
            #end if
        #if $updated_sam
            &&
            if [ -f outdir/telescope-updated.bam ] ; then
                samtools sort -T "\${TMPDIR:-.}" outdir/telescope-updated.bam > '$updated_alignment' ;
            else
                echo 'Updated alignment file not found.' ;
                exit 1 ;
            fi
        #end if