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comparison stringtie.xml @ 2:520e0988ec1c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
author iuc
date Thu, 14 May 2015 12:30:29 -0400
parents 9f80c71f1779
children df42808cc33a
comparison
equal deleted inserted replaced
1:9f80c71f1779 2:520e0988ec1c
1 <tool id="stringtie" name="StringTie" version="1.0.1"> 1 <tool id="stringtie" name="StringTie" version="1.0.3">
2 <description>RNA-Seq assembler</description> 2 <description>transcript assembly and quantification</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">stringtie</requirement> 4 <requirement type="package" version="1.0.3">stringtie</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 stringtie "$input_bam" 7 stringtie "$input_bam"
8 -o "$output_gtf" 8 -o "$output_gtf"
9 -p "\${GALAXY_SLOTS:-1}" 9 -p "\${GALAXY_SLOTS:-1}"
25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming 25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
26 #end if 26 #end if
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <param format="bam" label="BAM file to assemble" name="input_bam" type="data" /> 30 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
31 <conditional name="guide"> 31 <conditional name="guide">
32 <param label="Use GFF file to guide assembly" name="use_guide" type="select"> 32 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
33 <option value="yes">Use GFF</option> 33 <option value="yes">Use GFF</option>
34 <option selected="True" value="no">Do not use GFF</option> 34 <option selected="True" value="no">Do not use GFF</option>
35 </param> 35 </param>
36 <when value="no" /> 36 <when value="no" />
37 <when value="yes"> 37 <when value="yes">
38 <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> 38 <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
39 <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> 39 <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
40 <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> 40 <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
41 </when> 41 </when>
42 </conditional> 42 </conditional>
43 <conditional name="option_set"> 43 <conditional name="option_set">
44 <param label="Options" name="options" type="select"> 44 <param label="Options" name="options" type="select">
45 <option selected="True" value="default">Use defaults</option> 45 <option selected="True" value="default">Use defaults</option>
46 <option value="advanced">Specify advanced options</option> 46 <option value="advanced">Specify advanced options</option>
47 </param> 47 </param>
48 <when value="default" /> 48 <when value="default" />
49 <when value="advanced"> 49 <when value="advanced">
50 <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> 50 <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
51 <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> 51 <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
52 <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> 52 <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
53 <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> 53 <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
54 <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> 54 <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
55 <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> 55 <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
56 <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> 56 <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
57 <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> 57 <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
58 <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" /> 58 <param help="-s" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
59 <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> 59 <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
60 <param help="(-M)" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> 60 <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
61 </when> 61 </when>
62 </conditional> 62 </conditional>
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
127 </test> 127 </test>
128 </tests> 128 </tests>
129 <help> 129 <help>
130 <![CDATA[ 130 <![CDATA[
131 StringTie v1.0.1 usage:
132 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
133 [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
134 [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
135 {-B | -b <dir_path>} [-e]
136 131
137 Assemble RNA-Seq alignments into potential transcripts. 132 **What it does?**
138 133
139 Options: 134 StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional *de novo* assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.
135
136 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
137
138 ------
139
140 StringTie has the following options::
141
140 -G reference annotation to use for guiding the assembly process (GTF/GFF3) 142 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
141 -l name prefix for output transcripts (default: STRG) 143 -l name prefix for output transcripts (default: STRG)
142 -f minimum isoform fraction (default: 0.1) 144 -f minimum isoform fraction (default: 0.1)
143 -m minimum assembled transcript length to report (default 200bp) 145 -m minimum assembled transcript length to report (default 200bp)
144 -o output path/file name for the assembled transcripts GTF (default: stdout) 146 -o output path/file name for the assembled transcripts GTF (default: stdout)