Mercurial > repos > iuc > colibread_mapsembler2

comparison macros.xml @ 5:71d60a931e2f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:42:40 +0000
parents 21f081b808ff
children e8a8cb93878a
comparison
equal deleted inserted replaced
4:21f081b808ff 5:71d60a931e2f
1 <macros> 1 <macros>
2 <token name="@DISCOSNP_VERSION@">2.5.4</token> 2 <token name="@DISCOSNP_VERSION@">2.5.4</token>
3
4 <token name="@PROFILE@">20.01</token>
3 5
4 <xml name="discosnp_requirements"> 6 <xml name="discosnp_requirements">
5 <requirements> 7 <requirements>
6 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement> 8 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
7 </requirements> 9 </requirements>
8 </xml> 10 </xml>
9 11
10 <token name="@discosnp_single_reads@"><![CDATA[ 12 <token name="@discosnp_single_for@"><![CDATA[
11 #for $input in $input_type_options.list_reads 13 #for $input in $input_type_options.list_reads:
12 #set $filename = os.path.basename(str($input)) + "." + $input.ext 14 ]]></token>
13 ln -sf '${input}' '${filename}' && 15
16 <token name="@discosnp_single_end_for@"><![CDATA[
14 echo '${filename}' >> input.lst && 17 echo '${filename}' >> input.lst &&
15 #end for 18 #end for
16 ]]></token> 19 ]]></token>
17 20
18 <token name="@discosnp_paired_reads@"><![CDATA[ 21 <token name="@single_reads@"><![CDATA[
19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) 22 #import re
23 #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
24 #if $input.ext.startswith('fasta'):
25 #set filename = $base_filename + ".fasta"
26 #else:
27 #set filename = $base_filename + ".fastq"
28 #end if
29 #if $input.ext.endswith('.gz'):
30 gunzip -c '${input}' > '${filename}' &&
31 #else:
32 ln -sf '${input}' '${filename}' &&
33 #end if
34 ]]></token>
20 35
21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext 36 <token name="@discosnp_paired_for@"><![CDATA[
22 ln -sf '${paired.forward}' '${filenameFWD}' && 37 #for $i, $paired in enumerate($input_type_options.list_paired_reads):
38 ]]></token>
23 39
24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext 40 <token name="@discosnp_paired_end_for@"><![CDATA[
25 ln -sf '${paired.reverse}' '${filenameREV}' && 41 echo '${forward}' > "paired_${i}.lst" &&
42 echo '${reverse}' >> "paired_${i}.lst" &&
43 echo "paired_${i}.lst" >> input.lst &&
44 #end for
45 ]]></token>
26 46
27 echo '${filenameFWD}' > "paired_${i}.lst" && 47 <token name="@paired_reads@"><![CDATA[
28 echo '${filenameREV}' >> "paired_${i}.lst" && 48 #set $base_forward = re.sub('[^\w_]', '_', $paired.forward.element_identifier)
29 echo "paired_${i}.lst" >> input.lst && 49 #if $paired.forward.ext.startswith('fasta'):
50 #set forward = $base_forward + ".fasta"
51 #else:
52 #set forward = $base_forward + ".fastq"
53 #end if
54 #if $paired.forward.ext.endswith('.gz'):
55 gunzip -c '$paired.forward' > '$forward' &&
56 #else:
57 ln -sf '${paired.forward}' '$forward' &&
58 #end if
30 59
31 #end for 60 #set $base_reverse = re.sub('[^\w_]', '_', $paired.reverse.element_identifier)
61 #if $paired.reverse.ext.startswith('fasta'):
62 #set reverse = $base_reverse + ".fasta"
63 #else:
64 #set reverse = $base_reverse + ".fastq"
65 #end if
66 #if $paired.reverse.ext.endswith('.gz'):
67 gunzip -c '$paired.reverse' > '$reverse' &&
68 #else:
69 ln -sf '${paired.reverse}' '$reverse' &&
70 #end if
32 ]]></token> 71 ]]></token>
33 72
34 <xml name="discosnp_inputs"> 73 <xml name="discosnp_inputs">
35 <conditional name="input_type_options"> 74 <conditional name="input_type_options">
36 <param name="input_type" type="select" label="Input options"> 75 <param name="input_type" type="select" label="Input options">
37 <option value="single">Single end reads</option> 76 <option value="single">Single end reads</option>
38 <option value="paired">Paired end reads</option> 77 <option value="paired">Paired end reads</option>
39 <option value="mix">Both single and paired reads</option> 78 <option value="mix">Both single and paired reads</option>
40 </param> 79 </param>
41 <when value="single"> 80 <when value="single">
42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> 81 <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
43 </when> 82 </when>
44 <when value="paired"> 83 <when value="paired">
45 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" /> 84 <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
46 </when> 85 </when>
47 <when value="mix"> 86 <when value="mix">
48 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> 87 <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
49 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/> 88 <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
50 </when> 89 </when>
51 </conditional> 90 </conditional>
52 </xml> 91 </xml>
53 92
54 <xml name="discosnp_options"> 93 <xml name="discosnp_options">
95 -k ${program_type_choice.k} 134 -k ${program_type_choice.k}
96 -s ${program_type_choice.s} 135 -s ${program_type_choice.s}
97 ]]></token> 136 ]]></token>
98 137
99 <xml name="lordec_inputs"> 138 <xml name="lordec_inputs">
100 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> 139 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq,fastq.gz" multiple="true" label="Short read FASTA/Q files" />
101 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> 140 <param argument="-i" type="data" format="fasta,fastq.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
102 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> 141 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
103 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> 142 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
104 </xml> 143 </xml>
105 144
106 <token name="@discosnp_help@"><![CDATA[ 145 <token name="@discosnp_help@"><![CDATA[