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comparison stringtie.xml @ 2:b9c548ed919f draft

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Uploaded updated tool wrapper for stringtie 1.0.1
author iuc
date Thu, 05 Mar 2015 10:57:35 -0500
parents ab4798cf6458
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1:ab4798cf6458 2:b9c548ed919f
1 <?xml version="1.0"?> 1 <tool id="stringtie" name="StringTie" version="1.0.1">
2 <tool name="StringTie" id="stringtie" version="1.0.0">
3 <description>RNA-Seq assembler</description> 2 <description>RNA-Seq assembler</description>
4 <requirements> 3 <requirements>
5 <requirement type="package" version="0.97">stringtie</requirement> 4 <requirement type="package" version="1.0.1">stringtie</requirement>
6 </requirements> 5 </requirements>
7 <command> 6 <command><![CDATA[
8 <![CDATA[
9 stringtie "$input_bam" 7 stringtie "$input_bam"
10 -o "$output_gtf" 8 -o "$output_gtf"
11 -p "\${GALAXY_SLOTS:-1}" 9 -p "\${GALAXY_SLOTS:-1}"
12 #if str($guide.use_guide) == 'yes': 10 #if str($guide.use_guide) == 'yes':
13 -G "$guide.guide_gff" $guide.input_estimation 11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
14 -C "$coverage" 12 #if str($guide.output_ballgown) == '-b':
13 $guide.output_ballgown `pwd`
14 #end if
15 #end if 15 #end if
16 #if str($option_set.options) == 'advanced': 16 #if str($option_set.options) == 'advanced':
17 -l "$option_set.name_prefix"
17 -f "$option_set.fraction" 18 -f "$option_set.fraction"
18 -m "$option_set.min_tlen" 19 -m "$option_set.min_tlen"
19 -a "$option_set.min_anchor_len" 20 -a "$option_set.min_anchor_len"
20 -j "$option_set.min_anchor_cov" 21 -j "$option_set.min_anchor_cov"
21 -c "$option_set.min_bundle_cov" 22 -c "$option_set.min_bundle_cov"
24 -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
25 #end if 26 #end if
26 ]]> 27 ]]>
27 </command> 28 </command>
28 <inputs> 29 <inputs>
29 <param name="input_bam" type="data" format="bam" label="BAM file to assemble" /> 30 <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
30 <conditional name="guide"> 31 <conditional name="guide">
31 <param name="use_guide" type="select" label="Use GFF file to guide assembly"> 32 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
32 <option value="yes">Use GFF</option> 33 <option value="yes">Use GFF</option>
33 <option value="no" selected="True">Do not use GFF</option> 34 <option selected="True" value="no">Do not use GFF</option>
34 </param> 35 </param>
35 <when value="no" /> 36 <when value="no" />
36 <when value="yes"> 37 <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 format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
38 <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" /> 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" />
39 </when> 41 </when>
40 </conditional> 42 </conditional>
41 <conditional name="option_set"> 43 <conditional name="option_set">
42 <param name="options" type="select" label="Options"> 44 <param label="Options" name="options" type="select">
43 <option value="default" selected="True">Use defaults</option> 45 <option selected="True" value="default">Use defaults</option>
44 <option value="advanced">Specify advanced options</option> 46 <option value="advanced">Specify advanced options</option>
45 </param> 47 </param>
46 <when value="default" /> 48 <when value="default" />
47 <when value="advanced"> 49 <when value="advanced">
48 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" /> 50 <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
49 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" /> 51 <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
50 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" /> 52 <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
51 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" /> 53 <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
52 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" /> 54 <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
53 <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" /> 55 <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
54 <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" /> 56 <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
55 <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" /> 57 <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
56 <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" /> 58 <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
57 <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" /> 59 <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
58 </when> 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>
59 </conditional> 62 </conditional>
60 </inputs> 63 </inputs>
61 <outputs> 64 <outputs>
62 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/> 65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
63 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage"> 66 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
64 <filter>guide['use_guide'] == "yes"</filter> 67 <filter>guide['use_guide'] == "yes"</filter>
68 </data>
69 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
70 <filter>guide['output_ballgown']</filter>
71 </data>
72 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
73 <filter>guide['output_ballgown']</filter>
74 </data>
75 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
76 <filter>guide['output_ballgown']</filter>
77 </data>
78 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
79 <filter>guide['output_ballgown']</filter>
80 </data>
81 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
82 <filter>guide['output_ballgown']</filter>
65 </data> 83 </data>
66 </outputs> 84 </outputs>
67 <tests> 85 <tests>
68 <test> 86 <test>
69 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" /> 87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
70 <param name="use_guide" value="no" /> 88 <param name="use_guide" value="no" />
71 <param name="options" value="default" /> 89 <param name="options" value="default" />
72 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" /> 90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
73 </test> 91 </test>
74 <test> 92 <test>
75 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" /> 93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
76 <param name="use_guide" value="no" /> 94 <param name="use_guide" value="no" />
77 <param name="options" value="advanced" /> 95 <param name="options" value="advanced" />
78 <param name="fraction" value="0.17" /> 96 <param name="fraction" value="0.17" />
79 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" /> 97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
98 </test>
99 <test>
100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
101 <param name="use_guide" value="yes" />
102 <param name="guide_gff" value="stringtie_in.gtf" />
103 <param name="options" value="default" />
104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
105 </test>
106 <test>
107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
108 <param name="use_guide" value="yes" />
109 <param name="guide_gff" value="stringtie_in.gtf" />
110 <param name="options" value="advanced" />
111 <param name="fraction" value="0.17" />
112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
113 </test>
114 <test>
115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
116 <param name="use_guide" value="yes" />
117 <param name="output_ballgown" value="yes" />
118 <param name="guide_gff" value="stringtie_in.gtf" />
119 <param name="options" value="default" />
120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
121 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
122 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
80 </test> 127 </test>
81 </tests> 128 </tests>
82 <help> 129 <help>
83 <![CDATA[ 130 <![CDATA[
84 StringTie v0.97 usage:: 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]
85 136
86 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>] 137 Assemble RNA-Seq alignments into potential transcripts.
87 [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens] 138
88 [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>] 139 Options:
89 140 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
90 Assemble RNA-Seq alignments into potential transcripts. 141 -l name prefix for output transcripts (default: STRG)
91 142 -f minimum isoform fraction (default: 0.1)
92 Options: 143 -m minimum assembled transcript length to report (default 200bp)
93 -G reference annotation to use for guiding the assembly process (GTF/GFF3) 144 -o output path/file name for the assembled transcripts GTF (default: stdout)
94 -l name prefix for output transcripts (default: STRG) 145 -a minimum anchor length for junctions (default: 10)
95 -f minimum isoform fraction (default: 0.15) 146 -j minimum junction coverage (default: 1)
96 -m minimum assembled transcript length to report (default 200bp) 147 -t disable trimming of predicted transcripts based on coverage
97 -o output file with the assembled transcripts (default: stdout) 148 (default: coverage trimming is enabled)
98 -a minimum anchor length for junctions (default: 10) 149 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
99 -j minimum junction coverage (default: 1) 150 -s coverage saturation threshold; further read alignments will be
100 -t disable trimming of predicted transcripts based on coverage (default: trimming enabled) 151 ignored in a region where a local coverage depth of <maxcov>
101 -c minimum bundle reads per bp coverage to consider for assembly (default: 2) 152 is reached (default: 1,000,000);
102 -s coverage saturation threshold; further read alignments will be 153 -v verbose (log bundle processing details)
103 ignored in a region where a local coverage depth of <maxcov> 154 -g gap between read mappings triggering a new bundle (default: 50)
104 is reached (default: 1,000,000); 155 -C output file with reference transcripts that are covered by reads
105 -e abundance estimation only of input transcripts (for -G option) 156 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
106 -g gap between read mappings triggering a new bundle (default: 50) 157 -p number of threads (CPUs) to use (default: 1)
107 -S more sensitive run (default: no) 158 -B enable output of Ballgown table files which will be created in the
108 -C output file with all transcripts in reference that are fully 159 same directory as the output GTF (requires -G, -o recommended)
109 covered by reads 160 -b enable output of Ballgown table files but these files will be
110 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) 161 created under the directory path given as <dir_path>
111 162 -e only estimates the abundance of given reference transcripts (requires -G)
112 ]]> 163 ]]>
113 </help> 164 </help>
165 <citations>
166 <citation type="doi">doi:10.1038/nbt.3122</citation>
167 </citations>
114 </tool> 168 </tool>