Mercurial > repos > artbio > mircounts

comparison mircounts.xml @ 6:543472c9e272 draft

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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
comparison
equal deleted inserted replaced
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"/>