Mercurial > repos > iuc > colibread_kissplice

annotate macros.xml @ 3:98734f82a87e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 45e32ab41e7cdc4e3dabe87f074f052667c22574"
author iuc
date Wed, 22 Jan 2020 17:28:53 -0500
parents d5b4404c4788
children ccc77612cbb9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
1 <macros>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
2 <xml name="discosnp_requirements">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
3 <requirements>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
4 <requirement type="package" version="2.3.0">discosnp</requirement>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
5 </requirements>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
6 </xml>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
7
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
8 <token name="@DISCOSNP_VERSION@">2.3.0</token>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
9
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
10 <token name="@discosnp_single_reads@"><![CDATA[
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
11 #for $input in $input_type_options.list_reads
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
12 #set $filename = os.path.basename(str($input)) + "." + $input.ext
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
13 ln -sf '${input}' '${filename}' &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
14 echo '${filename}' >> input.lst &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
15 #end for
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
16 ]]></token>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
17
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
18 <token name="@discosnp_paired_reads@"><![CDATA[
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
20
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
22 ln -sf '${paired.forward}' '${filenameFWD}' &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
23
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
25 ln -sf '${paired.reverse}' '${filenameREV}' &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
26
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
27 echo '${filenameFWD}' > "paired_${i}.lst" &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
28 echo '${filenameREV}' >> "paired_${i}.lst" &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
29 echo "paired_${i}.lst" >> input.lst &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
30
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
31 #end for
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
32 ]]></token>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
33
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
34 <xml name="discosnp_inputs">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
35 <conditional name="input_type_options">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
36 <param name="input_type" type="select" label="Input options">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
37 <option value="single">Single end reads</option>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
38 <option value="paired">Paired end reads</option>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
39 <option value="mix">Both single and paired reads</option>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
40 </param>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
41 <when value="single">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
43 </when>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
44 <when value="paired">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
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" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
46 </when>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
47 <when value="mix">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
48 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
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"/>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
50 </when>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
51 </conditional>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
52 </xml>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
53
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
54 <xml name="discosnp_options">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
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"/>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
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"/>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
57 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
58 <param argument="-k" type="integer" label="Size of kmers" value="31" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
59
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
60 <conditional name="coverage_options_type" >
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
61 <param name="coverage_options" type="select" label="Coverage option">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
62 <option value="auto"></option>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
63 <option value="custom"></option>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
64 </param>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
65 <when value="auto" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
66 <when value="custom">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
67 <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
68 </when>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
69 </conditional>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
70
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
73
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
74 </xml>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
75
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
76 <token name="@discosnp_inputs@"><![CDATA[
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
77 -r input.lst
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
78 -b ${b}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
79 -D ${D}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
80 -P ${P}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
81 ${low_complexity}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
82 -k ${k}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
83
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
84 #if str($coverage_options_type.coverage_options) == 'auto'
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
85 -c auto
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
86 #else
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
87 -c '${coverage_options_type.c}'
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
88 #end if
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
89 -C ${C}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
90 -d ${d}
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
91 ]]></token>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
92
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
93 <token name="@lordec_inputs@"><![CDATA[
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
94 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
95 -i '${program_type_choice.i}'
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
96 -k ${program_type_choice.k}
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
97 -s ${program_type_choice.s}
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
98 ]]></token>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
99
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
100 <xml name="lordec_inputs">
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
101 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
102 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
103 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
104 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
105 </xml>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
106
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
107 <token name="@discosnp_help@"><![CDATA[
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
108 -------
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
109
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
110 .. class:: warningmark
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
111
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
112 **Input parameters**
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
113
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
114 -Sequences files in fasta or fastq each allele will be counted in each file individually
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
115
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
116 -Use collections: data list and/or data list paired
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
117
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
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
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
119
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
120 -------
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
121
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
122 .. class:: warningmark
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
123
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
124 **Ouput parameters**
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
125
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
126 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
127
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
128 -Fasta file with sequence extensions around the SNP.
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
129
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
130
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
131 -------
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
132
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
133 **Web site**
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
134
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
135 https://colibread.inria.fr/software/discosnp/
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
136
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
137 ]]></token>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
138
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
139 <xml name="citations">
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
140 <citations>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
141 <yield/>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
142 <citation type="doi">10.1186/s13742-015-0105-2</citation>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
143 </citations>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
144 </xml>
1
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
145
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
146 <xml name="discosnp_citation">
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
147 <citation type="doi">10.1101/209965</citation>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
148 </xml>
d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents: 0
diff changeset
149
0
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
150 </macros>