Mercurial > repos > iuc > stringtie
annotate stringtie.xml @ 4:df42808cc33a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
| author | iuc |
|---|---|
| date | Wed, 12 Aug 2015 07:07:40 -0400 |
| parents | 520e0988ec1c |
| children | f504b3b7e49d |
| rev | line source |
|---|---|
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
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1 <tool id="stringtie" name="StringTie" version="1.0.4"> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
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2 <description>transcript assembly and quantification</description> |
| 0 | 3 <requirements> |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
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4 <requirement type="package" version="1.0.4">stringtie</requirement> |
| 0 | 5 </requirements> |
| 1 | 6 <command><![CDATA[ |
| 0 | 7 stringtie "$input_bam" |
| 8 -o "$output_gtf" | |
| 9 -p "\${GALAXY_SLOTS:-1}" | |
| 10 #if str($guide.use_guide) == 'yes': | |
| 1 | 11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation |
| 12 #if str($guide.output_ballgown) == '-b': | |
| 13 $guide.output_ballgown `pwd` | |
| 14 #end if | |
| 0 | 15 #end if |
| 16 #if str($option_set.options) == 'advanced': | |
| 1 | 17 -l "$option_set.name_prefix" |
| 0 | 18 -f "$option_set.fraction" |
| 19 -m "$option_set.min_tlen" | |
| 20 -a "$option_set.min_anchor_len" | |
| 21 -j "$option_set.min_anchor_cov" | |
| 22 -c "$option_set.min_bundle_cov" | |
| 23 -s "$option_set.maxcov" | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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24 -g "$option_set.bdist" |
| 0 | 25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming |
| 26 #end if | |
| 27 ]]> | |
| 28 </command> | |
| 29 <inputs> | |
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2
520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
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30 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> |
| 0 | 31 <conditional name="guide"> |
| 1 | 32 <param label="Use GFF file to guide assembly" name="use_guide" type="select"> |
| 0 | 33 <option value="yes">Use GFF</option> |
| 1 | 34 <option selected="True" value="no">Do not use GFF</option> |
| 0 | 35 </param> |
| 36 <when value="no" /> | |
| 37 <when value="yes"> | |
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2
520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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38 <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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39 <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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40 <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> |
| 0 | 41 </when> |
| 42 </conditional> | |
| 43 <conditional name="option_set"> | |
| 1 | 44 <param label="Options" name="options" type="select"> |
| 45 <option selected="True" value="default">Use defaults</option> | |
| 0 | 46 <option value="advanced">Specify advanced options</option> |
| 47 </param> | |
| 48 <when value="default" /> | |
| 49 <when value="advanced"> | |
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2
520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
50 <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
51 <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
52 <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
53 <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
54 <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
55 <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
56 <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
57 <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
58 <param help="-s" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" /> |
|
520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
59 <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
|
60 <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> |
| 1 | 61 </when> |
| 0 | 62 </conditional> |
| 63 </inputs> | |
| 64 <outputs> | |
| 1 | 65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> |
| 66 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> | |
| 0 | 67 <filter>guide['use_guide'] == "yes"</filter> |
| 68 </data> | |
| 1 | 69 <data format="tabular" from_work_dir="e_data.ctab" label="${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> | |
| 83 </data> | |
| 0 | 84 </outputs> |
| 85 <tests> | |
| 86 <test> | |
| 1 | 87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 0 | 88 <param name="use_guide" value="no" /> |
| 89 <param name="options" value="default" /> | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 0 | 91 </test> |
| 92 <test> | |
| 1 | 93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 0 | 94 <param name="use_guide" value="no" /> |
| 95 <param name="options" value="advanced" /> | |
| 96 <param name="fraction" value="0.17" /> | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 1 | 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" /> | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 1 | 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" /> | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 1 | 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" /> | |
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4
df42808cc33a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
iuc
parents:
2
diff
changeset
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125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 1 | 126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> |
| 0 | 127 </test> |
| 128 </tests> | |
| 129 <help> | |
| 130 <![CDATA[ | |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
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131 |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
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132 **What it does?** |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
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133 |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
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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. |
| 0 | 135 |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
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136 .. _StringTie: http://ccb.jhu.edu/software/stringtie/ |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
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137 |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
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138 ------ |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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139 |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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140 StringTie has the following options:: |
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520e0988ec1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a
iuc
parents:
1
diff
changeset
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141 |
| 1 | 142 -G reference annotation to use for guiding the assembly process (GTF/GFF3) |
| 143 -l name prefix for output transcripts (default: STRG) | |
| 144 -f minimum isoform fraction (default: 0.1) | |
| 145 -m minimum assembled transcript length to report (default 200bp) | |
| 146 -o output path/file name for the assembled transcripts GTF (default: stdout) | |
| 147 -a minimum anchor length for junctions (default: 10) | |
| 148 -j minimum junction coverage (default: 1) | |
| 149 -t disable trimming of predicted transcripts based on coverage | |
| 150 (default: coverage trimming is enabled) | |
| 151 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5) | |
| 152 -s coverage saturation threshold; further read alignments will be | |
| 153 ignored in a region where a local coverage depth of <maxcov> | |
| 154 is reached (default: 1,000,000); | |
| 155 -v verbose (log bundle processing details) | |
| 156 -g gap between read mappings triggering a new bundle (default: 50) | |
| 157 -C output file with reference transcripts that are covered by reads | |
| 158 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) | |
| 159 -p number of threads (CPUs) to use (default: 1) | |
| 160 -B enable output of Ballgown table files which will be created in the | |
| 161 same directory as the output GTF (requires -G, -o recommended) | |
| 162 -b enable output of Ballgown table files but these files will be | |
| 163 created under the directory path given as <dir_path> | |
| 164 -e only estimates the abundance of given reference transcripts (requires -G) | |
| 165 ]]> | |
| 166 </help> | |
| 167 <citations> | |
| 168 <citation type="doi">doi:10.1038/nbt.3122</citation> | |
| 169 </citations> | |
| 170 </tool> |