Mercurial > repos > iuc > stringtie
comparison 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 |
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| 3:48b891c1c2aa | 4:df42808cc33a |
|---|---|
| 1 <tool id="stringtie" name="StringTie" version="1.0.3"> | 1 <tool id="stringtie" name="StringTie" version="1.0.4"> |
| 2 <description>transcript assembly and quantification</description> | 2 <description>transcript assembly and quantification</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.0.3">stringtie</requirement> | 4 <requirement type="package" version="1.0.4">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}" |
| 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 "$option_set.maxcov" | 23 -s "$option_set.maxcov" |
| 24 -g "$option_set.bdist" | 24 -g "$option_set.bdist" |
| 25 -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 |
| 26 #end if | 26 #end if |
| 27 ]]> | 27 ]]> |
| 28 </command> | 28 </command> |
| 29 <inputs> | 29 <inputs> |
| 85 <tests> | 85 <tests> |
| 86 <test> | 86 <test> |
| 87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> | 87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 88 <param name="use_guide" value="no" /> | 88 <param name="use_guide" value="no" /> |
| 89 <param name="options" value="default" /> | 89 <param name="options" value="default" /> |
| 90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" /> | 90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 91 </test> | 91 </test> |
| 92 <test> | 92 <test> |
| 93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> | 93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 94 <param name="use_guide" value="no" /> | 94 <param name="use_guide" value="no" /> |
| 95 <param name="options" value="advanced" /> | 95 <param name="options" value="advanced" /> |
| 96 <param name="fraction" value="0.17" /> | 96 <param name="fraction" value="0.17" /> |
| 97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" /> | 97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 98 </test> | 98 </test> |
| 99 <test> | 99 <test> |
| 100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> | 100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 101 <param name="use_guide" value="yes" /> | 101 <param name="use_guide" value="yes" /> |
| 102 <param name="guide_gff" value="stringtie_in.gtf" /> | 102 <param name="guide_gff" value="stringtie_in.gtf" /> |
| 103 <param name="options" value="default" /> | 103 <param name="options" value="default" /> |
| 104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" /> | 104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 105 </test> | 105 </test> |
| 106 <test> | 106 <test> |
| 107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> | 107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 108 <param name="use_guide" value="yes" /> | 108 <param name="use_guide" value="yes" /> |
| 109 <param name="guide_gff" value="stringtie_in.gtf" /> | 109 <param name="guide_gff" value="stringtie_in.gtf" /> |
| 110 <param name="options" value="advanced" /> | 110 <param name="options" value="advanced" /> |
| 111 <param name="fraction" value="0.17" /> | 111 <param name="fraction" value="0.17" /> |
| 112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" /> | 112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 113 </test> | 113 </test> |
| 114 <test> | 114 <test> |
| 115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> | 115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> |
| 116 <param name="use_guide" value="yes" /> | 116 <param name="use_guide" value="yes" /> |
| 117 <param name="output_ballgown" value="yes" /> | 117 <param name="output_ballgown" value="yes" /> |
| 120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> | 120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> |
| 121 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_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" /> | 122 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> |
| 123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> | 123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> |
| 124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_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" /> | 125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> |
| 126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> | 126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> |
| 127 </test> | 127 </test> |
| 128 </tests> | 128 </tests> |
| 129 <help> | 129 <help> |
| 130 <![CDATA[ | 130 <![CDATA[ |