Mercurial > repos > iuc > data_manager_hisat2_index_builder

comparison data_manager/hisat2_index_builder.xml @ 5:8eac26f44d29 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
author iuc
date Mon, 18 Nov 2019 17:22:30 -0500
parents d210e1f185bd
children
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4:d210e1f185bd 5:8eac26f44d29
1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.0.5"> 1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.1.0" profile="19.05">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.5">hisat2</requirement> 4 <requirement type="package" version="2.1.0">hisat2</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: 7 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input:
8 ln -s '${advanced.gtf_input}' gtf_file.gtf && 8 ln -s '${advanced.gtf_input}' gtf_file.gtf &&
9 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt && 9 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt &&
64 <param name="sequence_id" type="text" value="" label="ID for sequence" /> 64 <param name="sequence_id" type="text" value="" label="ID for sequence" />
65 </inputs> 65 </inputs>
66 <outputs> 66 <outputs>
67 <data name="out_file" format="data_manager_json" /> 67 <data name="out_file" format="data_manager_json" />
68 </outputs> 68 </outputs>
69 <tests>
70 <test>
71 <param name="all_fasta_source" value="phiX174"/>
72 <output name="out_file" file="hisat2_data_manager.json"/>
73 </test>
74 </tests>
69 <help> 75 <help>
70 <![CDATA[ 76 <![CDATA[
71 .. class:: infomark 77 .. class:: infomark
72 78
73 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 79 **Notice:** If you leave name, description, or id blank, it will be generated automatically.