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comparison stringtie.xml @ 5:f504b3b7e49d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
author iuc
date Wed, 21 Oct 2015 16:07:42 -0400
parents df42808cc33a
children d0bb240d7525
comparison
equal deleted inserted replaced
4:df42808cc33a 5:f504b3b7e49d
1 <tool id="stringtie" name="StringTie" version="1.0.4"> 1 <tool id="stringtie" name="StringTie" version="1.1.0">
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.4">stringtie</requirement> 4 <requirement type="package" version="1.1.0">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}"
18 -f "$option_set.fraction" 18 -f "$option_set.fraction"
19 -m "$option_set.min_tlen" 19 -m "$option_set.min_tlen"
20 -a "$option_set.min_anchor_len" 20 -a "$option_set.min_anchor_len"
21 -j "$option_set.min_anchor_cov" 21 -j "$option_set.min_anchor_cov"
22 -c "$option_set.min_bundle_cov" 22 -c "$option_set.min_bundle_cov"
23 -s "$option_set.maxcov"
24 -g "$option_set.bdist" 23 -g "$option_set.bdist"
25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming 24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
25 #if $option_set.A:
26 -A "$gene_abundance_estimation"
27 #end if
28 #if str($option_set.x).strip() != "":
29 -x "$option_set.x"
30 #end if
26 #end if 31 #end if
27 ]]> 32 ]]>
28 </command> 33 </command>
29 <inputs> 34 <inputs>
30 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> 35 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
53 <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> 58 <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" /> 59 <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" /> 60 <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" /> 61 <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" /> 62 <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" />
59 <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> 63 <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" /> 64 <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
65 <param argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
66 <param argument="-A" truevalue="-A" falsevalue="" type="boolean" help="" label="Additional gene abundance estimation output file" />
61 </when> 67 </when>
62 </conditional> 68 </conditional>
63 </inputs> 69 </inputs>
64 <outputs> 70 <outputs>
65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 71 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
72 <data format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
73 <filter>option_set['A']</filter>
74 </data>
66 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> 75 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
67 <filter>guide['use_guide'] == "yes"</filter> 76 <filter>guide['use_guide'] == "yes"</filter>
68 </data> 77 </data>
69 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression"> 78 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
70 <filter>guide['output_ballgown']</filter> 79 <filter>guide['output_ballgown']</filter>
123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> 132 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> 133 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 134 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 135 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
127 </test> 136 </test>
137 <test>
138 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
139 <param name="use_guide" value="yes" />
140 <param name="guide_gff" value="stringtie_in.gtf" />
141 <param name="options" value="advanced" />
142 <param name="fraction" value="0.17" />
143 <param name="A" value="True" />
144 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
145 <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" />
146 </test>
147 <test>
148 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
149 <param name="use_guide" value="yes" />
150 <param name="guide_gff" value="stringtie_in.gtf" />
151 <param name="options" value="advanced" />
152 <param name="fraction" value="0.15" />
153 <param name="c" value="test_chromosome" />
154 <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
155 </test>
128 </tests> 156 </tests>
129 <help> 157 <help>
130 <![CDATA[ 158 <![CDATA[
131 159
132 **What it does?** 160 **What it does?**
140 StringTie has the following options:: 168 StringTie has the following options::
141 169
142 -G reference annotation to use for guiding the assembly process (GTF/GFF3) 170 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
143 -l name prefix for output transcripts (default: STRG) 171 -l name prefix for output transcripts (default: STRG)
144 -f minimum isoform fraction (default: 0.1) 172 -f minimum isoform fraction (default: 0.1)
145 -m minimum assembled transcript length to report (default 200bp) 173 -m minimum assembled transcript length (default: 200)
146 -o output path/file name for the assembled transcripts GTF (default: stdout) 174 -o output path/file name for the assembled transcripts GTF (default: stdout)
147 -a minimum anchor length for junctions (default: 10) 175 -a minimum anchor length for junctions (default: 10)
148 -j minimum junction coverage (default: 1) 176 -j minimum junction coverage (default: 1)
149 -t disable trimming of predicted transcripts based on coverage 177 -t disable trimming of predicted transcripts based on coverage
150 (default: coverage trimming is enabled) 178 (default: coverage trimming is enabled)
151 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5) 179 -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) 180 -v verbose (log bundle processing details)
156 -g gap between read mappings triggering a new bundle (default: 50) 181 -g gap between read mappings triggering a new bundle (default: 50)
157 -C output file with reference transcripts that are covered by reads 182 -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) 183 -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) 184 -p number of threads (CPUs) to use (default: 1)
160 -B enable output of Ballgown table files which will be created in the 185 -B enable output of Ballgown table files which will be created in the
161 same directory as the output GTF (requires -G, -o recommended) 186 same directory as the output GTF (requires -G, -o recommended)
162 -b enable output of Ballgown table files but these files will be 187 -b enable output of Ballgown table files but these files will be
163 created under the directory path given as <dir_path> 188 created under the directory path given as <dir_path>
164 -e only estimates the abundance of given reference transcripts (requires -G) 189 -e only estimates the abundance of given reference transcripts (requires -G)
190 -A gene abundance estimation output file
191 -x do not assemble any transcripts on these reference sequence(s)
192
193
165 ]]> 194 ]]>
166 </help> 195 </help>
167 <citations> 196 <citations>
168 <citation type="doi">doi:10.1038/nbt.3122</citation> 197 <citation type="doi">doi:10.1038/nbt.3122</citation>
169 </citations> 198 </citations>