Mercurial > repos > matthias > stacks2_clonefilter

annotate stacks_clonefilter.xml @ 2:223e7778451a 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/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Fri, 30 Nov 2018 07:42:16 -0500
parents a46a0b4b297d
children 4758a347d62e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
223e7778451a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents: 0
diff changeset
1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
0
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
2 <description>Identify PCR clones</description>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
3 <macros>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
4 <import>macros.xml</import>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
5 </macros>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
6 <expand macro="requirements"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
7 <expand macro="stdio"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
8 <expand macro="version_cmd"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
9 <command><![CDATA[
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
10
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
11 #if $data_type.dt_select == "single"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
12
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
13 #if $data_type.fname.is_of_type('fastqsanger')
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
14 #set $ext = ".fq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
15 #set inputype = "fastq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
16 #else
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
17 #set $ext = ".fq.gz"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
18 #set inputype = "gzfastq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
19 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
20
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
21 ln -s '$data_type.fname' R1$ext &&
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
22 #else
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
23
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
24 #if $data_type.fwd.is_of_type('fastqsanger')
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
25 #set $ext = ".fq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
26 #set inputype = "fastq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
27 #else
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
28 #set $ext = ".fq.gz"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
29 #set inputype = "gzfastq"
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
30 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
31
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
32 ln -s '$data_type.fwd' R1$ext &&
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
33 ln -s '$data_type.rev' R2$ext &&
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
34 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
35
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
36
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
37 mkdir clone_outputs
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
38
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
39 &&
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
40
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
41 clone_filter
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
42 #if $data_type.dt_select == 'single':
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
43 -f R1$ext
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
44 #else
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
45 -1 R1$ext
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
46 -2 R2$ext
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
47 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
48
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
49 -i $inputype
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
50
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
51 -o clone_outputs
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
52 $capture
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
53
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
54 #if $oligo_len_1
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
55 --oligo_len_1 $oligo_len_1
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
56 $data_type.barcode_encoding
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
57 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
58 #if $oligo_len_2
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
59 --oligo_len_2 $oligo_len_2
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
60 #end if
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
61 $retain_oligo
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
62 ## only supports fastq.gz output since the
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
63 ## the program outputs empty files for fasta/fastq
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
64 -y gzfastq
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
65
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
66 ]]></command>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
67 <inputs>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
68 <conditional name="data_type">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
69 <param name="dt_select" type="select" label="Single or Paired-end">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
70 <option value="single">Single</option>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
71 <option value="pair">Pair</option>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
72 </param>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
73 <when value="single">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
74 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
75 <param name="barcode_encoding" type="select" label="Barcode location">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
76 <expand macro="barcode_encoding_single" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
77 </param>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
78
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
79 </when>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
80 <when value="pair">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
81 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
82 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
83 <param name="barcode_encoding" type="select" label="Barcode location">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
84 <expand macro="barcode_encoding_pair" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
85 </param>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
86 </when>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
87 </conditional>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
88 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
89 <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
90 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
91 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
92
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
93 </inputs>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
94 <outputs>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
95 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
96 <filter>data_type['dt_select'] == 'single'</filter>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
97 </data>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
98
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
99 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
100 <filter>data_type['dt_select'] == 'pair'</filter>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
101 </data>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
102 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
103 <filter>data_type['dt_select'] == 'pair'</filter>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
104 </data>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
105 </outputs>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
106 <tests>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
107 <test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
108 <conditional name="data_type">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
109 <param name="dt_select" value="single" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
110 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
111 </conditional>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
112 <param name="oligo_len_1" value="6" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
113 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
114 </test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
115 <test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
116 <conditional name="data_type">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
117 <param name="dt_select" value="single" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
118 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
119 <param name="barcode_encoding" value="--index_null" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
120 </conditional>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
121 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
122 </test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
123 <test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
124 <conditional name="data_type">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
125 <param name="dt_select" value="pair" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
126 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
127 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
128 </conditional>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
129 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
130 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
131 </test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
132 <test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
133 <conditional name="data_type">
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
134 <param name="dt_select" value="pair" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
135 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
136 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
137 </conditional>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
138 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
139 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
140 </test>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
141 </tests>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
142 <help>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
143 <![CDATA[
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
144 .. class:: infomark
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
145
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
146
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
147 The clone_filter program is designed to identify PCR clones.
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
148
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
149 @STACKS_INFOS@
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
150 ]]>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
151 </help>
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
152 <expand macro="citation" />
a46a0b4b297d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
diff changeset
153 </tool>