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comparison stringtie.xml @ 27:95d141564e5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 8923485156dc1150213ad1f324aa16aaef4ae643
author iuc
date Mon, 31 Oct 2022 20:07:17 +0000
parents d8424a4f39ed
children 9b48a7386627
comparison
equal deleted inserted replaced
26:d8424a4f39ed 27:95d141564e5d
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 #import re 13 #import re
14 #set $compressed = ("bam","cram")
14 mkdir -p ./special_de_output/sample1/ && 15 mkdir -p ./special_de_output/sample1/ &&
15 16
16 ## Get Guide GTF/GFF if selected 17 ## Get Guide GTF/GFF if selected
17 18
18 #if str($guide.use_guide) == 'yes': 19 #if str($guide.use_guide) == 'yes':
32 #if $input_options.input_mode == 'long_reads' 33 #if $input_options.input_mode == 'long_reads'
33 -L 34 -L
34 -E $input_options.error_splice 35 -E $input_options.error_splice
35 #end if 36 #end if
36 #else 37 #else
37 #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam': 38 #if $input_options.input_bam_short.file_ext in $compressed and $input_options.input_bam_long.file_ext in $compressed:
38 strigtie '$input_options.input_bam_short' '$input_options.input_bam_long' 39 stringtie '$input_options.input_bam_short' '$input_options.input_bam_long'
39 #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam': 40 #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype in $compressed:
40 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam 41 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
41 && stringtie short_sorted.sam '$input_options.input_bam_long' 42 && stringtie short_sorted.sam '$input_options.input_bam_long'
42 #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam': 43 #else if $input_options.input_bam_short.metadata.ftype in $compressed and $input_options.input_bam_long.metadata.ftype == 'sam':
43 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam 44 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
44 && stringtie'$input_options.input_bam_short' long_sorted.sam 45 && stringtie'$input_options.input_bam_short' long_sorted.sam
45 #else 46 #else
46 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam 47 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
47 && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam 48 && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
141 <option value="short_reads">Short reads</option> 142 <option value="short_reads">Short reads</option>
142 <option value="long_reads">Long reads</option> 143 <option value="long_reads">Long reads</option>
143 <option value="mixed_reads">Mixed mode: short and long reads</option> 144 <option value="mixed_reads">Mixed mode: short and long reads</option>
144 </param> 145 </param>
145 <when value="short_reads"> 146 <when value="short_reads">
146 <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"/> 147 <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"/>
147 </when> 148 </when>
148 <when value="long_reads"> 149 <when value="long_reads">
149 <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"/> 150 <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"/>
150 <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" /> 151 <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" />
151 </when> 152 </when>
152 <when value="mixed_reads"> 153 <when value="mixed_reads">
153 <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"/> 154 <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"/>
154 <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"/> 155 <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"/>
155 <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" /> 156 <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" />
156 </when> 157 </when>
157 </conditional> 158 </conditional>
158 <param name="rna_strandness" type="select" label="Specify strand information" 159 <param name="rna_strandness" type="select" label="Specify strand information"
159 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"> 160 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">
416 <param name="input_bam_short" ftype="bam" value="short_reads.bam" /> 417 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
417 <param name="input_bam_long" ftype="bam" value="long_reads.bam" /> 418 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
418 </conditional> 419 </conditional>
419 <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/> 420 <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
420 </test> 421 </test>
422 <!-- Test cram input -->
423 <test expect_num_outputs="1">
424 <conditional name="input_options">
425 <param name="input_mode" value="mixed_reads"/>
426 <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" />
427 <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />
428 </conditional>
429 <output name="output_gtf" ftype="gtf">
430 <assert_contents>
431 <has_text text="gi|251831106|ref|NC_012920.1|"/>
432 <has_text text="StringTie version 2.2.1"/>
433 </assert_contents>
434 </output>
435 </test>
421 </tests> 436 </tests>
422 <help><![CDATA[ 437 <help><![CDATA[
423 438
424 .. class:: infomark 439 .. class:: infomark
425 440