Mercurial > repos > artbio > mircounts
comparison mircounts.xml @ 6:543472c9e272 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
| author | artbio |
|---|---|
| date | Tue, 05 Sep 2017 17:54:46 -0400 |
| parents | 9ea96a02c416 |
| children | 65befdc9925a |
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| 5:9ea96a02c416 | 6:543472c9e272 |
|---|---|
| 1 <tool id="mircounts" name="miRcounts" version="1.0.0"> | 1 <tool id="mircounts" name="miRcounts" version="1.1.0"> |
| 2 <description> Counts miRNA alignments from small RNA sequence data</description> | 2 <description> Counts miRNA alignments from small RNA sequence data</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.18">gnu-wget</requirement> | 4 <requirement type="package" version="1.18">gnu-wget</requirement> |
| 5 <requirement type="package" version="1.2">bowtie</requirement> | 5 <requirement type="package" version="1.2">bowtie</requirement> |
| 6 <requirement type="package" version="1.4.1">samtools</requirement> | 6 <requirement type="package" version="1.4.1">samtools</requirement> |
| 83 <option value="0">0</option> | 83 <option value="0">0</option> |
| 84 <option selected="true" value="1">1</option> | 84 <option selected="true" value="1">1</option> |
| 85 <option value="2">2</option> | 85 <option value="2">2</option> |
| 86 <option value="3">3</option> | 86 <option value="3">3</option> |
| 87 </param> | 87 </param> |
| 88 <param help="Output mature Mir counts" label="Output mature Mir counts" | |
| 89 name="output_mir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" /> | |
| 90 <param help="Output pre-Mir counts" label="Output pre-Mir counts" | |
| 91 name="output_premir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" /> | |
| 88 <conditional name="plotting"> | 92 <conditional name="plotting"> |
| 89 <param label="Additional miRNA charts" name="plottingOption" type="select"> | 93 <param label="Additional miRNA charts" name="plottingOption" type="select"> |
| 90 <option value="no">no</option> | 94 <option value="no">no</option> |
| 91 <option value="yes" selected="True">yes</option> | 95 <option value="yes" selected="True">yes</option> |
| 92 </param> | 96 </param> |
| 99 <when value="no"> | 103 <when value="no"> |
| 100 </when> | 104 </when> |
| 101 </conditional> | 105 </conditional> |
| 102 </inputs> | 106 </inputs> |
| 103 <outputs> | 107 <outputs> |
| 104 <data format="bam" label="BAM alignment" name="output" /> | 108 <data format="bam" label="BAM alignment" name="output" hidden="true" /> |
| 105 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/> | 109 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3" hidden="true" /> |
| 106 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file"> | 110 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file"> |
| 111 <filter>output_premir_counts == True</filter> | |
| 107 <actions> | 112 <actions> |
| 108 <action name="column_names" type="metadata" default="Gene,Counts" /> | 113 <action name="column_names" type="metadata" default="Gene,Counts" /> |
| 109 </actions> | 114 </actions> |
| 110 </data> | 115 </data> |
| 111 <data format="tabular" label="Mir Counts" name="mir_count_file"> | 116 <data format="tabular" label="Mir Counts" name="mir_count_file"> |
| 117 <filter>output_mir_counts == True</filter> | |
| 112 <actions> | 118 <actions> |
| 113 <action name="column_names" type="metadata" default="Gene,Counts" /> | 119 <action name="column_names" type="metadata" default="Gene,Counts" /> |
| 114 </actions> | 120 </actions> |
| 115 </data> | 121 </data> |
| 116 <data format="tabular" label="Coverage Table" name="coverage_dataframe"> | 122 <data format="tabular" label="Coverage Table" name="coverage_dataframe"> |
| 130 <param name="v" value="0"/> | 136 <param name="v" value="0"/> |
| 131 <param name="genomeKey" value="dme"/> | 137 <param name="genomeKey" value="dme"/> |
| 132 <param name="mirbase_version" value="CURRENT"/> | 138 <param name="mirbase_version" value="CURRENT"/> |
| 133 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 139 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 134 <param name="plottingOption" value="no"/> | 140 <param name="plottingOption" value="no"/> |
| 141 <param name="output_premir_counts" value="True"/> | |
| 142 <param name="output_mir_counts" value="True"/> | |
| 135 <output name="output" file="unclipped.out.bam" ftype="bam"/> | 143 <output name="output" file="unclipped.out.bam" ftype="bam"/> |
| 136 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 144 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> |
| 137 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 145 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> |
| 138 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 146 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> |
| 139 </test> | 147 </test> |
| 147 <param name="genomeKey" value="dme"/> | 155 <param name="genomeKey" value="dme"/> |
| 148 <param name="mirbase_version" value="CURRENT"/> | 156 <param name="mirbase_version" value="CURRENT"/> |
| 149 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 157 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 150 <param name="plottingOption" value="yes"/> | 158 <param name="plottingOption" value="yes"/> |
| 151 <param name="display" value="relative"/> | 159 <param name="display" value="relative"/> |
| 160 <param name="output_premir_counts" value="True"/> | |
| 161 <param name="output_mir_counts" value="True"/> | |
| 152 <output name="output" file="unclipped.out.bam" ftype="bam"/> | 162 <output name="output" file="unclipped.out.bam" ftype="bam"/> |
| 153 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 163 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> |
| 154 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 164 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> |
| 155 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 165 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> |
| 156 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> | 166 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> |
| 162 <param name="genomeKey" value="dme"/> | 172 <param name="genomeKey" value="dme"/> |
| 163 <param name="mirbase_version" value="CURRENT"/> | 173 <param name="mirbase_version" value="CURRENT"/> |
| 164 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> | 174 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> |
| 165 <param name="plottingOption" value="yes"/> | 175 <param name="plottingOption" value="yes"/> |
| 166 <param name="display" value="absolute"/> | 176 <param name="display" value="absolute"/> |
| 177 <param name="output_premir_counts" value="True"/> | |
| 178 <param name="output_mir_counts" value="True"/> | |
| 167 <output name="output" file="clipped.out.bam" ftype="bam"/> | 179 <output name="output" file="clipped.out.bam" ftype="bam"/> |
| 168 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 180 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> |
| 169 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> | 181 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> |
| 170 <output name="mir_count_file" file="mirs_clipped_count.tab"/> | 182 <output name="mir_count_file" file="mirs_clipped_count.tab"/> |
| 171 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/> | 183 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/> |