Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 11:72aade318318 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749"
author iuc
date Thu, 20 May 2021 12:56:42 +0000
parents bfc70c8cc5ca
children 39b40a9a6296
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10:bfc70c8cc5ca 11:72aade318318
1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01"> 1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description> 2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
3 3 <macros>
4 <requirements> 4 <import>macros.xml</import>
5 <requirement type="package" version="4.1.1">repeatmasker</requirement> 5 </macros>
6 </requirements> 6 <expand macro='xrefs'/>
7 7 <expand macro='edam_ontology' />
8 <command detect_errors="exit_code"><![CDATA[ 8 <expand macro='requirements' />
9 <version_command>repeatmasker --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[
9 RM_PATH=\$(which RepeatMasker) && 11 RM_PATH=\$(which RepeatMasker) &&
10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && 12 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
11 13
12 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && 14 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
13 #if $repeat_source.source_type == "dfam_up": 15 #if $repeat_source.source_type == "dfam_up":
95 <option value="yes" selected="true">Yes</option> 97 <option value="yes" selected="true">Yes</option>
96 <option value="no">No</option> 98 <option value="no">No</option>
97 </param> 99 </param>
98 <when value="yes"> 100 <when value="yes">
99 <param name="species_list" type="select" label="Species"> 101 <param name="species_list" type="select" label="Species">
100 <option value="vertebrate">Vertebrate (other than below)</option> 102 <option value="human" selected="true">Human (Homo sapiens)</option>
101 <option value="mammal">Mammal (other than below)</option> 103 <option value="rodent">Rodent (Order Rodentia)</option>
102 <option value="human" selected="true">Human</option> 104 <option value="mouse">Mouse (Mus musculus)</option>
103 <option value="rodent">Rodent</option> 105 <option value="rattus">Rat (Rattus sp.)</option>
104 <option value="mouse">Mouse</option>
105 <option value="rat">Rat</option>
106 <option value="danio">Danio (zebra fish)</option> 106 <option value="danio">Danio (zebra fish)</option>
107 <option value="drosophila">Fruit fly (Drosophila melanogaster)</option> 107 <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
108 <option value="elegans">Caenorhabditis elegans (nematode)</option> 108 <option value="elegans">Caenorhabditis elegans (nematode)</option>
109 </param> 109 </param>
110 </when> 110 </when>
217 <output name="output_masked_genome" file="small_dfam_up.fasta.masked" /> 217 <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />
218 <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" /> 218 <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />
219 <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" /> 219 <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
220 <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/> 220 <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
221 </test> 221 </test>
222 <test expect_num_outputs="4">
223 <param name="input_fasta" value="small.fasta" ftype="fasta" />
224 <param name="source_type" value="dfam" />
225 <param name="species_list" value="rattus" />
226 <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />
227 <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />
228 <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />
229 <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>
230 </test>
222 </tests> 231 </tests>
223 <help><![CDATA[ 232 <help><![CDATA[
224 RepeatMasker is a program that screens DNA for interspersed repeats and low 233 RepeatMasker is a program that screens DNA for interspersed repeats and low
225 complexity DNA sequences. The database of repeats to screen for can be 234 complexity DNA sequences. The database of repeats to screen for can be
226 provided as a FASTA file or downloaded from RepBase_. If the RepBase option is 235 provided as a FASTA file or downloaded from RepBase_. If the RepBase option is
232 241
233 .. _RepBase: http://www.girinst.org/repbase/ 242 .. _RepBase: http://www.girinst.org/repbase/
234 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html 243 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
235 ]]> 244 ]]>
236 </help> 245 </help>
237 <citations> 246 <expand macro="citations" />
238 <citation type="bibtex">
239 @misc{RepeatMasker,
240 title = {RepeatMasker Open-4.0},
241 howpublished = {\url{http://www.repeatmasker.org}},
242 author = {Smit, AFA and Hubley, R and Green, P.},
243 year = {2013-2015}}
244 </citation>
245 </citations>
246 </tool> 247 </tool>