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comparison stringtie.xml @ 0:f5c030adcded draft

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Imported from capsule None
author devteam
date Tue, 01 Jul 2014 19:08:39 -0400
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1 <?xml version="1.0"?>
2 <tool name="StringTie" id="stringtie" version="1.0.0">
3 <description>RNA-Seq assembler</description>
4 <requirements>
5 <requirement type="package" version="0.97">stringtie</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 stringtie "$input_bam"
10 -o "$output_gtf"
11 -p "\${GALAXY_SLOTS:-1}"
12 #if str($guide.use_guide) == 'yes':
13 -G "$guide.guide_gff" $guide.input_estimation
14 -C "$coverage"
15 #end if
16 #if str($option_set.options) == 'advanced':
17 -f "$option_set.fraction"
18 -m "$option_set.min_tlen"
19 -a "$option_set.min_anchor_len"
20 -j "$option_set.min_anchor_cov"
21 -c "$option_set.min_bundle_cov"
22 -s "$option_set.maxcov"
23 -g "$option_set.bdist"
24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
25 #end if
26 ]]>
27 </command>
28 <inputs>
29 <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />
30 <conditional name="guide">
31 <param name="use_guide" type="select" label="Use GFF file to guide assembly">
32 <option value="yes">Use GFF</option>
33 <option value="no" selected="True">Do not use GFF</option>
34 </param>
35 <when value="no" />
36 <when value="yes">
37 <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" />
38 <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" />
39 </when>
40 </conditional>
41 <conditional name="option_set">
42 <param name="options" type="select" label="Options">
43 <option value="default" selected="True">Use defaults</option>
44 <option value="advanced">Specify advanced options</option>
45 </param>
46 <when value="default" />
47 <when value="advanced">
48 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />
49 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />
50 <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" />
51 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
52 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />
53 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />
54 <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" />
55 <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
56 <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" />
57 <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
58 <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
59 </when>
60 </conditional>
61 </inputs>
62 <outputs>
63 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/>
64 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
65 <filter>guide['use_guide'] == "yes"</filter>
66 </data>
67 </outputs>
68 <tests>
69 <test>
70 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
71 <param name="use_guide" value="no" />
72 <param name="options" value="default" />
73 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" />
74 </test>
75 <test>
76 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
77 <param name="use_guide" value="no" />
78 <param name="options" value="advanced" />
79 <param name="fraction" value="0.17" />
80 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" />
81 </test>
82 </tests>
83 <help>
84 <![CDATA[
85 StringTie v0.97 usage::
86
87 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>]
88 [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
89 [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
90
91 Assemble RNA-Seq alignments into potential transcripts.
92
93 Options:
94 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
95 -l name prefix for output transcripts (default: STRG)
96 -f minimum isoform fraction (default: 0.15)
97 -m minimum assembled transcript length to report (default 200bp)
98 -o output file with the assembled transcripts (default: stdout)
99 -a minimum anchor length for junctions (default: 10)
100 -j minimum junction coverage (default: 1)
101 -t disable trimming of predicted transcripts based on coverage (default: trimming enabled)
102 -c minimum bundle reads per bp coverage to consider for assembly (default: 2)
103 -s coverage saturation threshold; further read alignments will be
104 ignored in a region where a local coverage depth of <maxcov>
105 is reached (default: 1,000,000);
106 -v verbose (log bundle processing details)
107 -e abundance estimation only of input transcripts (for -G option)
108 -g gap between read mappings triggering a new bundle (default: 50)
109 -S more sensitive run (default: no)
110 -C output file with all transcripts in reference that are fully
111 covered by reads
112 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
113 -p number of threads (CPUs) to use (default: 1)
114
115 ]]>
116 </help>
117 </tool>