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comparison fargene.xml @ 1:239ce9f24386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
author iuc
date Mon, 02 Dec 2019 04:39:18 -0500
parents 6f743c615c41
children b982a9ea939c
comparison
equal deleted inserted replaced
0:6f743c615c41 1:239ce9f24386
1 <tool id="fargene" name="fargene" version="@VERSION@"> 1 <tool id="fargene" name="fargene" version="@VERSION@+galaxy1">
2 <description>Fragmented antibiotic resistance gene identifier </description> 2 <description>Fragmented antibiotic resistance gene identifier </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
68 #if $store_peptides: 68 #if $store_peptides:
69 '$store_peptides' 69 '$store_peptides'
70 #end if 70 #end if
71 && 71 &&
72 #if $inputs.input_type in ('paired', 'collection'): 72 #if $inputs.input_type in ('paired', 'collection'):
73 tar czf retrievedFragments.tar.gz fargene_output/retrievedFragments 73 tar -czf retrievedFragments.tar.gz fargene_output/retrievedFragments
74 #end if 74 #end if
75 2>&1 75 2>&1
76 ]]> </command> 76 ]]> </command>
77 <inputs> 77 <inputs>
78 <conditional name="inputs"> 78 <conditional name="inputs">
129 <filter>inputs["input_type"] in ['paired' , 'collection']</filter> 129 <filter>inputs["input_type"] in ['paired' , 'collection']</filter>
130 </data> 130 </data>
131 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)"> 131 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)">
132 </data> 132 </data>
133 <collection name="hmmsearchresults" type="list" label="HMM Search Result"> 133 <collection name="hmmsearchresults" type="list" label="HMM Search Result">
134 <discover_datasets pattern="__name__" directory="fargene_output/hmmsearchresults" format="txt" ext="out" visible="false" /> 134 <discover_datasets pattern="(?P&lt;name&gt;.+).out" directory="fargene_output/hmmsearchresults" format="txt" visible="false" />
135 </collection> 135 </collection>
136 <collection name="predictedGenes" type="list" label="Predicted Genes"> 136 <collection name="predictedGenes" type="list" label="Predicted Genes">
137 <discover_datasets pattern="__name__" directory="fargene_output/predictedGenes" ext="fasta" format="fasta" visible="false" /> 137 <discover_datasets pattern="(?P&lt;name&gt;.+).fasta" directory="fargene_output/predictedGenes" format="fasta" visible="false" />
138 </collection> 138 </collection>
139 </outputs> 139 </outputs>
140 <tests> 140 <tests>
141 <test expect_num_outputs="5"> 141 <test expect_num_outputs="5">
142 <conditional name="inputs"> 142 <conditional name="inputs">