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comparison stringtie.xml @ 7:e3f369973054 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
author iuc
date Mon, 18 Jul 2016 06:50:04 -0400
parents d0bb240d7525
children c84d44519b2e
comparison
equal deleted inserted replaced
6:d0bb240d7525 7:e3f369973054
77 </conditional> 77 </conditional>
78 </inputs> 78 </inputs>
79 <outputs> 79 <outputs>
80 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 80 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
81 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation"> 81 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
82 <filter>option_set['abundance_estimation']</filter> 82 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
83 </data> 83 </data>
84 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> 84 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
85 <filter>guide['use_guide'] == "yes"</filter> 85 <filter>guide['use_guide'] == 'yes'</filter>
86 </data> 86 </data>
87 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression"> 87 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
88 <filter>guide['output_ballgown']</filter> 88 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
89 </data> 89 </data>
90 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression"> 90 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
91 <filter>guide['output_ballgown']</filter> 91 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
92 </data> 92 </data>
93 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression"> 93 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
94 <filter>guide['output_ballgown']</filter> 94 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
95 </data> 95 </data>
96 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping"> 96 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
97 <filter>guide['output_ballgown']</filter> 97 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
98 </data> 98 </data>
99 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping"> 99 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
100 <filter>guide['output_ballgown']</filter> 100 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
101 </data> 101 </data>
102 </outputs> 102 </outputs>
103 <tests> 103 <tests>
104 <test> 104 <test>
105 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 105 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
202 202
203 ]]> 203 ]]>
204 </help> 204 </help>
205 <expand macro="citations" /> 205 <expand macro="citations" />
206 </tool> 206 </tool>
207