Mercurial > repos > iuc > rgrnastar

comparison macros.xml @ 11:41929aa1e7f3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
author iuc
date Sat, 17 Aug 2019 09:38:21 -0400
parents d82339e37e8e
children 39bde80cd248
comparison
equal deleted inserted replaced
10:d82339e37e8e 11:41929aa1e7f3
19 <requirement type="package" version="@VERSION@">star</requirement> 19 <requirement type="package" version="@VERSION@">star</requirement>
20 <requirement type="package" version="1.9">samtools</requirement> 20 <requirement type="package" version="1.9">samtools</requirement>
21 </requirements> 21 </requirements>
22 </xml> 22 </xml>
23 23
24 <xml name="index_selection" token_with_gene_model="1"> 24 <xml name="index_selection" token_with_gene_model="0">
25 <param argument="--genomeDir" name="genomeDir" type="select" 25 <param argument="--genomeDir" name="genomeDir" type="select"
26 label="Select reference genome" 26 label="Select reference genome"
27 help="If your genome of interest is not listed, contact the Galaxy team"> 27 help="If your genome of interest is not listed, contact the Galaxy team">
28 <options from_data_table="rnastar_index2_versioned"> 28 <options from_data_table="rnastar_index2_versioned">
29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> 29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
125 <when value="indexed"> 125 <when value="indexed">
126 <conditional name="GTFconditional"> 126 <conditional name="GTFconditional">
127 <param name="GTFselect" type="select" 127 <param name="GTFselect" type="select"
128 label="Reference genome with or without an annotation" 128 label="Reference genome with or without an annotation"
129 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> 129 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
130 <option value="without-gtf">use genome reference with builtin gene-model</option> 130 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
131 <option value="with-gtf">use genome reference without builtin gene-model</option> 131 <option value="with-gtf">use genome reference with builtin gene-model</option>
132 </param> 132 </param>
133 <when value="with-gtf"> 133 <when value="with-gtf">
134 <expand macro="index_selection" with_gene_model="0" /> 134 <expand macro="index_selection" with_gene_model="1" />
135 <expand macro="@SJDBOPTIONS@" /> 135 <expand macro="@SJDBOPTIONS@" />
136 </when> 136 </when>
137 <when value="without-gtf"> 137 <when value="without-gtf">
138 <expand macro="index_selection" with_gene_model="1" /> 138 <expand macro="index_selection" with_gene_model="0" />
139 </when> 139 </when>
140 </conditional> 140 </conditional>
141 </when> 141 </when>
142 <when value="history"> 142 <when value="history">
143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> 143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />