Mercurial > repos > iuc > chira_map

comparison chira_map.xml @ 17:7925dd016f53 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
author iuc
date Sun, 19 Dec 2021 15:48:59 +0000
parents 95ddee768b61
children
comparison
equal deleted inserted replaced
16:95ddee768b61 17:7925dd016f53
1 <tool id="chira_map" name="ChiRA map" version="@WRAPPER_VERSION@0"> 1 <tool id="chira_map" name="ChiRA map" version="@TOOL_VERSION@0">
2 <description>map reads to trascriptome</description> 2 <description>map reads to trascriptome</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 chira_map.py -b 9 chira_map.py -b
10 -a '$alignment.aligner' 10 -a '$alignment.aligner'
11 -i '$query' 11 -i '$query'
121 <param name="aligner" value="bwa"/> 121 <param name="aligner" value="bwa"/>
122 <param name="query" value="reads.fasta"/> 122 <param name="query" value="reads.fasta"/>
123 <param name="ref_type" value="split"/> 123 <param name="ref_type" value="split"/>
124 <param name="ref_fasta1" value="ref1.fasta"/> 124 <param name="ref_fasta1" value="ref1.fasta"/>
125 <param name="ref_fasta2" value="ref2.fasta"/> 125 <param name="ref_fasta2" value="ref2.fasta"/>
126 <param name="unmapped" value="True"/>
127 <output name="mapped_bed" > 126 <output name="mapped_bed" >
128 <assert_contents> 127 <assert_contents>
129 <has_text_matching expression="mmu-miR-6898-5p\t11\t21\t2\|2,mmu-miR-6898-5p,11,21,\+,10M39S\t1\t\+" /> 128 <has_text_matching expression="mmu-miR-6898-5p\t11\t21\t2\|2,mmu-miR-6898-5p,11,21,\+,10M39S\t1\t\+" />
130 </assert_contents> 129 </assert_contents>
131 </output> 130 </output>
140 <param name="aligner" value="clan"/> 139 <param name="aligner" value="clan"/>
141 <param name="query" value="reads.fasta"/> 140 <param name="query" value="reads.fasta"/>
142 <param name="ref_type" value="split"/> 141 <param name="ref_type" value="split"/>
143 <param name="ref_fasta1" value="ref1.fasta"/> 142 <param name="ref_fasta1" value="ref1.fasta"/>
144 <param name="ref_fasta2" value="ref2.fasta"/> 143 <param name="ref_fasta2" value="ref2.fasta"/>
145 <param name="unmapped" value="True"/>
146 <output name="mapped_bed" > 144 <output name="mapped_bed" >
147 <assert_contents> 145 <assert_contents>
148 <has_text_matching expression="mmu-miR-20a-5p\t0\t23\t3\|2,mmu-miR-20a-5p,0,23,\+,5S23M27S\t1\t\+" /> 146 <has_text_matching expression="mmu-miR-20a-5p\t0\t23\t3\|2,mmu-miR-20a-5p,0,23,\+,5S23M27S\t1\t\+" />
149 </assert_contents> 147 </assert_contents>
150 </output> 148 </output>
165 * An optional second reference fasta file, incase if you split your reference into two 163 * An optional second reference fasta file, incase if you split your reference into two
166 164
167 **Output** 165 **Output**
168 166
169 * BED file containing the alignments 167 * BED file containing the alignments
170 * Optional unmapped FASTA file 168 * unmapped FASTA file (only for aligner BWA-MEM)
171 169
172 </help> 170 </help>
173 <expand macro="citations" /> 171 <expand macro="citations" />
174 </tool> 172 </tool>