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comparison macros.xml @ 4:92a66ccb7e6c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
author iuc
date Fri, 18 Aug 2023 09:22:33 +0000
parents cc7863bec4e0
children
comparison
equal deleted inserted replaced
3:cc7863bec4e0 4:92a66ccb7e6c
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.6.1</token> 2 <token name="@TOOL_VERSION@">0.6.1</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
8 </requirements> 8 </requirements>
116 <option value="paired">Paired end</option> 116 <option value="paired">Paired end</option>
117 <option value="paired_collection" selected="true">Paired collection</option> 117 <option value="paired_collection" selected="true">Paired collection</option>
118 <option value="interleaved">Interleaved</option> 118 <option value="interleaved">Interleaved</option>
119 </param> 119 </param>
120 </xml> 120 </xml>
121 <xml name="paired_reads">
122 <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
123 </xml>
124 <xml name="individual_assembly_reads"> 121 <xml name="individual_assembly_reads">
125 <conditional name="read_type"> 122 <conditional name="read_type">
126 <expand macro="read_type"/> 123 <expand macro="read_type"/>
127 <when value="single"> 124 <when value="single">
128 <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" /> 125 <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" />
130 <when value="paired"> 127 <when value="paired">
131 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" /> 128 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" />
132 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" /> 129 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
133 </when> 130 </when>
134 <when value="paired_collection"> 131 <when value="paired_collection">
135 <expand macro="paired_reads"/> 132 <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
136 </when> 133 </when>
137 <when value="interleaved"> 134 <when value="interleaved">
138 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" /> 135 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
139 </when> 136 </when>
140 </conditional> 137 </conditional>
166 #set $fn = "fw/" + $id 163 #set $fn = "fw/" + $id
167 #silent $fw_fp.append( $fn ) 164 #silent $fw_fp.append( $fn )
168 ln -s '$reads.paired_reads.forward' '$fn' && 165 ln -s '$reads.paired_reads.forward' '$fn' &&
169 #set $fn = "rv/" + $id 166 #set $fn = "rv/" + $id
170 #silent $rv_fp.append( $fn ) 167 #silent $rv_fp.append( $fn )
171 ln -s '$mreads.paired_reads.reverse' '${fn}' && 168 ln -s '$reads.paired_reads.reverse' '$fn' &&
172 #else if $reads.type == 'interleaved' 169 #else if $reads.type == 'interleaved'
173 #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier)) 170 #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
174 #silent $interl_fp.append( $fn ) 171 #silent $interl_fp.append( $fn )
175 ln -s '$reads.interleaved' '$fn' && 172 ln -s '$reads.interleaved' '$fn' &&
176 #end if 173 #end if
204 <when value="paired"> 201 <when value="paired">
205 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" /> 202 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" />
206 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" /> 203 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
207 </when> 204 </when>
208 <when value="paired_collection"> 205 <when value="paired_collection">
209 <expand macro="paired_reads"/> 206 <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
210 </when> 207 </when>
211 <when value="interleaved"> 208 <when value="interleaved">
212 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" /> 209 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
213 </when> 210 </when>
214 </conditional> 211 </conditional>