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comparison macros.xml @ 1:dc31aacc886b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author iuc
date Fri, 24 Nov 2017 12:45:22 -0500
parents 0b9a713ece1d
children a4d4b2564a2a
comparison
equal deleted inserted replaced
0:0b9a713ece1d 1:dc31aacc886b
1 <macros> 1 <macros>
2 <xml name="discosnp_requirements">
3 <requirements>
4 <requirement type="package" version="2.3.0">discosnp</requirement>
5 </requirements>
6 </xml>
7
8 <token name="@DISCOSNP_VERSION@">2.3.0</token>
9
2 <token name="@discosnp_single_reads@"><![CDATA[ 10 <token name="@discosnp_single_reads@"><![CDATA[
3 #for $input in $input_type_options.list_reads 11 #for $input in $input_type_options.list_reads
4 #set $filename = str($input) + "." + $input.ext 12 #set $filename = os.path.basename(str($input)) + "." + $input.ext
5 ln -sf '${input}' '${filename}' && 13 ln -sf '${input}' '${filename}' &&
6 echo '${filename}' >> input.lst && 14 echo '${filename}' >> input.lst &&
7 #end for 15 #end for
8 ]]></token> 16 ]]></token>
17
9 <token name="@discosnp_paired_reads@"><![CDATA[ 18 <token name="@discosnp_paired_reads@"><![CDATA[
10 #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) 19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
11 20
12 #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext 21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
13 ln -sf '${paired.forward}' '${filenameFWD}' && 22 ln -sf '${paired.forward}' '${filenameFWD}' &&
14 23
15 #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext 24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
16 ln -sf '${paired.reverse}' '${filenameREV}' && 25 ln -sf '${paired.reverse}' '${filenameREV}' &&
17 26
18 echo '${filenameFWD}' > "paired_${i}.lst" && 27 echo '${filenameFWD}' > "paired_${i}.lst" &&
19 echo '${filenameREV}' >> "paired_${i}.lst" && 28 echo '${filenameREV}' >> "paired_${i}.lst" &&
20 echo "paired_${i}.lst" >> input.lst && 29 echo "paired_${i}.lst" >> input.lst &&
21 30
22 #end for 31 #end for
23 ]]></token> 32 ]]></token>
33
34 <xml name="discosnp_inputs">
35 <conditional name="input_type_options">
36 <param name="input_type" type="select" label="Input options">
37 <option value="single">Single end reads</option>
38 <option value="paired">Paired end reads</option>
39 <option value="mix">Both single and paired reads</option>
40 </param>
41 <when value="single">
42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
43 </when>
44 <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" />
46 </when>
47 <when value="mix">
48 <param name='list_reads' argument="-r" format="fasta,fastq" 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"/>
50 </when>
51 </conditional>
52 </xml>
53
54 <xml name="discosnp_options">
55 <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/>
56 <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/>
57 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
58 <param argument="-k" type="integer" label="Size of kmers" value="31" />
59
60 <conditional name="coverage_options_type" >
61 <param name="coverage_options" type="select" label="Coverage option">
62 <option value="auto"></option>
63 <option value="custom"></option>
64 </param>
65 <when value="auto" />
66 <when value="custom">
67 <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
68 </when>
69 </conditional>
70
71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
73
74 </xml>
75
76 <token name="@discosnp_inputs@"><![CDATA[
77 -r input.lst
78 -b ${b}
79 -D ${D}
80 -P ${P}
81 ${low_complexity}
82 -k ${k}
83
84 #if str($coverage_options_type.coverage_options) == 'auto'
85 -c auto
86 #else
87 -c '${coverage_options_type.c}'
88 #end if
89 -C ${C}
90 -d ${d}
91 ]]></token>
92
24 <token name="@lordec_inputs@"><![CDATA[ 93 <token name="@lordec_inputs@"><![CDATA[
25 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }" 94 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
26 -i '${program_type_choice.i}' 95 -i '${program_type_choice.i}'
27 -k ${program_type_choice.k} 96 -k ${program_type_choice.k}
28 -s ${program_type_choice.s} 97 -s ${program_type_choice.s}
29 ]]></token> 98 ]]></token>
99
30 <xml name="lordec_inputs"> 100 <xml name="lordec_inputs">
31 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> 101 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
32 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> 102 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
33 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> 103 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
34 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> 104 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
35 </xml> 105 </xml>
106
107 <token name="@discosnp_help@"><![CDATA[
108 -------
109
110 .. class:: warningmark
111
112 **Input parameters**
113
114 -Sequences files in fasta or fastq each allele will be counted in each file individually
115
116 -Use collections: data list and/or data list paired
117
118 -Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
119
120 -------
121
122 .. class:: warningmark
123
124 **Ouput parameters**
125
126 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
127
128 -Fasta file with sequence extensions around the SNP.
129
130
131 -------
132
133 **Web site**
134
135 https://colibread.inria.fr/software/discosnp/
136
137 ]]></token>
138
36 <xml name="citations"> 139 <xml name="citations">
37 <citations> 140 <citations>
38 <yield/> 141 <yield/>
39 <citation type="doi">10.1186/s13742-015-0105-2</citation> 142 <citation type="doi">10.1186/s13742-015-0105-2</citation>
40 </citations> 143 </citations>
41 </xml> 144 </xml>
145
146 <xml name="discosnp_citation">
147 <citation type="doi">10.1101/209965</citation>
148 </xml>
149
42 </macros> 150 </macros>