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comparison stringtie.xml @ 17:1ebd14235b92 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit afa107c23e8eb889f0ed3469e2c897447be6bbf8"
author iuc
date Tue, 25 Feb 2020 18:07:47 -0500
parents eba36e001f45
children 258d696dbd7e
comparison
equal deleted inserted replaced
16:eba36e001f45 17:1ebd14235b92
19 ln -s '$guide.guide_source.ref_builtin.fields.path' guide.gff && 19 ln -s '$guide.guide_source.ref_builtin.fields.path' guide.gff &&
20 #end if 20 #end if
21 #end if 21 #end if
22 22
23 #if $input_bam.metadata.ftype == 'sam': 23 #if $input_bam.metadata.ftype == 'sam':
24 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie 24 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' -T "\${TMPDIR:-.}" | stringtie
25 #else 25 #else
26 stringtie '$input_bam' 26 stringtie '$input_bam'
27 #end if 27 #end if
28
29 $long_reads
28 30
29 -o '$output_gtf' 31 -o '$output_gtf'
30 -p "\${GALAXY_SLOTS:-1}" 32 -p "\${GALAXY_SLOTS:-1}"
31 33
32 $rna_strandness 34 $rna_strandness
108 #end if 110 #end if
109 #end if 111 #end if
110 ]]></command> 112 ]]></command>
111 <inputs> 113 <inputs>
112 <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/> 114 <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>
115 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Input contains long reads?" help="Select if the input contains long error-prone reads, e.g. from Oxford Nanopore or PacBio sequencing."/>
113 <param name="rna_strandness" type="select" label="Specify strand information" 116 <param name="rna_strandness" type="select" label="Specify strand information"
114 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"> 117 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">
115 <option value="" selected="true">Unstranded</option> 118 <option value="" selected="true">Unstranded</option>
116 <option value="--fr">Forward (FR)</option> 119 <option value="--fr">Forward (FR)</option>
117 <option value="--rf">Reverse (RF)</option> 120 <option value="--rf">Reverse (RF)</option>