Mercurial > repos > devteam > bowtie_wrappers
comparison bowtie_wrapper.xml @ 7:2c811e06006a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 397bc85634156862fdaa3d74b8f1e53752876619
author | devteam |
---|---|
date | Thu, 04 May 2017 14:59:54 -0400 |
parents | ecbbc8be6266 |
children |
comparison
equal
deleted
inserted
replaced
6:ecbbc8be6266 | 7:2c811e06006a |
---|---|
1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0"> | 1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0"> |
2 <description></description> | |
2 <requirements> | 3 <requirements> |
3 <requirement type="package" version="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.2.0">bowtie</requirement> |
4 </requirements> | 5 </requirements> |
5 <description></description> | |
6 <version_command>bowtie --version</version_command> | 6 <version_command>bowtie --version</version_command> |
7 <command> | 7 <command> |
8 python '$__tool_directory__/bowtie_wrapper.py' | 8 python '$__tool_directory__/bowtie_wrapper.py' |
9 ## Set number of threads | 9 ## Set number of threads |
10 --threads="\${GALAXY_SLOTS:-4}" | 10 --threads="\${GALAXY_SLOTS:-4}" |
165 <validator type="no_options" message="No indexes are available" /> | 165 <validator type="no_options" message="No indexes are available" /> |
166 </options> | 166 </options> |
167 </param> | 167 </param> |
168 </when> | 168 </when> |
169 <when value="history"> | 169 <when value="history"> |
170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> | 170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> |
171 <conditional name="indexParams"> | 171 <conditional name="indexParams"> |
172 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> | 172 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> |
173 <option value="indexPreSet">Default</option> | 173 <option value="indexPreSet">Default</option> |
174 <option value="indexFull">Set your own</option> | 174 <option value="indexFull">Set your own</option> |
175 </param> | 175 </param> |
311 </conditional> <!-- sParams --> | 311 </conditional> <!-- sParams --> |
312 </when> <!-- single --> | 312 </when> <!-- single --> |
313 <when value="paired"> | 313 <when value="paired"> |
314 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> | 314 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> |
315 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> | 315 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> |
316 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> | 316 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> |
317 <column name="name" index="0"/> | 317 <column name="name" index="0"/> |
318 <column name="value" index="0"/> | 318 <column name="value" index="0"/> |
319 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> | 319 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> |
320 </options> | 320 </options> |
321 </param> | 321 </param> |