comparison stringtie.xml @ 21:914cfcba0ec8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 8923485156dc1150213ad1f324aa16aaef4ae643

20:cef79931dda5

    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
#import re
mkdir -p ./special_de_output/sample1/ &&

## Get Guide GTF/GFF if selected

#if str($guide.use_guide) == 'yes':

    #if $input_options.input_mode == 'long_reads'
        -L
        -E $input_options.error_splice
    #end if
#else
    #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam':
        strigtie '$input_options.input_bam_short' '$input_options.input_bam_long'
    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam':
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
        && stringtie short_sorted.sam '$input_options.input_bam_long'
    #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam':
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
        && stringtie'$input_options.input_bam_short' long_sorted.sam
    #else
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
        && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam

                <option value="short_reads">Short reads</option>
                <option value="long_reads">Long reads</option>
                <option value="mixed_reads">Mixed mode: short and long reads</option>
            </param>
            <when value="short_reads">
                <param name="input_bam" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
            </when>
            <when value="long_reads">
                <param name="input_bam" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
            </when>
            <when value="mixed_reads">
                <param name="input_bam_short" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
                <param name="input_bam_long" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
            </when>
        </conditional>
        <param name="rna_strandness" type="select" label="Specify strand information"
            help="Select 'Forward (FR)' if your reads are from a forward-stranded library, 'Reverse (RF)' if your reads are from a reverse-stranded library, or 'Unstranded' if your reads are not from a stranded library. See Help section below for more information. Default: Unstranded">

                <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
            </conditional>            
            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

21:914cfcba0ec8

    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
#import re
#set $compressed = ("bam","cram")
mkdir -p ./special_de_output/sample1/ &&

## Get Guide GTF/GFF if selected

#if str($guide.use_guide) == 'yes':

    #if $input_options.input_mode == 'long_reads'
        -L
        -E $input_options.error_splice
    #end if
#else
    #if $input_options.input_bam_short.file_ext in $compressed and $input_options.input_bam_long.file_ext in $compressed:
        stringtie '$input_options.input_bam_short' '$input_options.input_bam_long'
    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype in $compressed:
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
        && stringtie short_sorted.sam '$input_options.input_bam_long'
    #else if $input_options.input_bam_short.metadata.ftype in $compressed and $input_options.input_bam_long.metadata.ftype == 'sam':
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
        && stringtie'$input_options.input_bam_short' long_sorted.sam
    #else
        samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
        && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam

                <option value="short_reads">Short reads</option>
                <option value="long_reads">Long reads</option>
                <option value="mixed_reads">Mixed mode: short and long reads</option>
            </param>
            <when value="short_reads">
                <param name="input_bam" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
            </when>
            <when value="long_reads">
                <param name="input_bam" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
            </when>
            <when value="mixed_reads">
                <param name="input_bam_short" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
                <param name="input_bam_long" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
            </when>
        </conditional>
        <param name="rna_strandness" type="select" label="Specify strand information"
            help="Select 'Forward (FR)' if your reads are from a forward-stranded library, 'Reverse (RF)' if your reads are from a reverse-stranded library, or 'Unstranded' if your reads are not from a stranded library. See Help section below for more information. Default: Unstranded">

                <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
            </conditional>            
            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!-- Test cram input -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="mixed_reads"/>
                <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" />
                <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />
            </conditional>            
            <output name="output_gtf" ftype="gtf">
                <assert_contents>
                    <has_text text="gi|251831106|ref|NC_012920.1|"/>
                    <has_text text="StringTie version 2.2.1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark