annotate fastx_clipper.xml @ 7:90858c306551 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:53:49 +0000
parents cb1e251cac37
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
90858c306551 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 6
diff changeset
1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.3+galaxy@VERSION_SUFFIX@" profile="22.05">
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
2 <description>adapter sequences</description>
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
3 <macros>
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
5 </macros>
5
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
6 <expand macro="requirements">
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
7 <requirement type="package" version="1.0.8">bzip2</requirement>
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
8 </expand>
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
10 @CATS@ fastx_clipper
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
11 -l $minlength
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
12 -a '$clip_source.clip_sequence'
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
13 -d $keepdelta
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
14 -v
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
15 $KEEP_N
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
16 $DISCARD_OPTIONS
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
17 @FQQUAL@
5
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
18 @GZIP@ > '$output'
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
19 ]]></command>
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
20
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
21 <inputs>
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
22 <expand macro="fastx_input" />
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
23
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
24 <param name="minlength" type="integer" value="15"
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
25 label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
26
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
27 <conditional name="clip_source">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
28 <param name="clip_source_list" type="select" label="Source">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
29 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
30 <option value="user">Enter custom sequence</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
31 </param>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
32
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
33 <when value="user">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
34 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
35 </when>
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
36
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
37 <when value="prebuilt">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
38 <param name="clip_sequence" type="select" label="Choose Adapter">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
39 <options from_file="fastx_clipper_sequences.txt">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
40 <column name="name" index="1"/>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
41 <column name="value" index="0"/>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
42 </options>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
43 </param>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
44 </when>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
45 </conditional>
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
46
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
47 <param name="keepdelta" type="integer" value="0"
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
48 label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
49 help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
50
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
51 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
52 <option value="">Yes</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
53 <option value="-n">No</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
54 </param>
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
55
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
56 <param name="DISCARD_OPTIONS" type="select" label="Output options">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
57 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
58 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
59 <option value="">Output both clipped and non-clipped sequences</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
60 </param>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
61 </inputs>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
62 <outputs>
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
63 <data name="output" format_source="input" metadata_source="input" />
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
64 </outputs>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
65 <tests>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
66 <test>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
67 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
68 <param name="minlength" value="15" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
69 <param name="clip_source_list" value="user" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
70 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
71 <param name="keepdelta" value="0" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
72 <param name="KEEP_N" value="-n" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
73 <param name="DISCARD_OPTIONS" value="-c" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
74 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
75 </test>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
76 </tests>
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
77 <help><![CDATA[
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
78 **What it does**
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
79
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
80 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
81
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
82 --------
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
83
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
84
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
85 **Clipping Illustration:**
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
86
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
87 .. image:: fastx_clipper_illustration.png
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
88
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
89 **Clipping Example:**
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
90
2
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
91 .. image:: fastx_clipper_example.png
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
92
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
93 **In the above example:**
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
94
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
95 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
96 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
97
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
98 ------
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
99
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
100 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
101
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
102 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
103 ]]></help>
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
104 <expand macro="citations" />
0
2fe2d2b9e8e4 Uploaded tool tarball.
devteam
parents:
diff changeset
105 </tool>