Mercurial > repos > devteam > fastx_clipper

annotate fastx_clipper.xml @ 2:4286abbc87a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:40:52 -0400
parents 08495cd1d93e
children 410c5d0b638a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
2 <description>adapter sequences</description>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
3 <requirements>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
5 </requirements>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
6 <command>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
7 <![CDATA[
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
8 zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
9 #if $input.ext == "fastqsanger":
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
10 -Q 33
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
11 #end if
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
12 ]]>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
13 </command>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
14
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
15 <inputs>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" />
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
17
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
18 <param name="minlength" type="integer" value="15">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
19 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
20 </param>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
21
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
22 <conditional name="clip_source">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
23 <param name="clip_source_list" type="select" label="Source">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
24 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
25 <option value="user">Enter custom sequence</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
26 </param>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
27
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
28 <when value="user">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
29 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
30 </when>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
31
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
32 <when value="prebuilt">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
33 <param name="clip_sequence" type="select" label="Choose Adapter">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
34 <options from_file="fastx_clipper_sequences.txt">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
35 <column name="name" index="1"/>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
36 <column name="value" index="0"/>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
37 </options>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
38 </param>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
39 </when>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
40 </conditional>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
41
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
42 <param name="keepdelta" type="integer" value="0">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
43 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
44 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
45 </param>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
46
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
47 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
48 <option value="">Yes</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
49 <option value="-n">No</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
50 </param>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
51
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
52 <param name="DISCARD_OPTIONS" type="select" label="Output options">
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
53 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
54 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
55 <option value="">Output both clipped and non-clipped sequences</option>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
56 </param>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
57 </inputs>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
58 <outputs>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
59 <data format_source="input" name="output" metadata_source="input" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
60 </outputs>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
61 <tests>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
62 <test>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
63 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
64 <param name="maxmismatches" value="2" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
65 <param name="minlength" value="15" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
66 <param name="clip_source_list" value="user" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
67 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
68 <param name="keepdelta" value="0" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
69 <param name="KEEP_N" value="-n" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
70 <param name="DISCARD_OPTIONS" value="-c" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
71 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
72 </test>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
73 </tests>
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
74 <help>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
75 **What it does**
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
76
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
77 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
78
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
79 --------
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
80
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
81
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
82 **Clipping Illustration:**
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
83
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
84 .. image:: fastx_clipper_illustration.png
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
85
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
86 **Clipping Example:**
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
87
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
88 .. image:: fastx_clipper_example.png
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
89
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
90 **In the above example:**
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
91
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
92 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
93 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
94
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
95 ------
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
96
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
97 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
98
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
99 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
2
4286abbc87a2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
100 </help>
0
743d895d28db Uploaded tool tarball.
devteam
parents:
diff changeset
101 </tool>