Mercurial > repos > devteam > fastx_clipper
comparison fastx_clipper.xml @ 2:bdf1ce174e39 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:38:51 -0500 |
parents | 8192b4014977 |
children | 85263dc18cec |
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1:8192b4014977 | 2:bdf1ce174e39 |
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1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" > | 1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1"> |
2 <description>adapter sequences</description> | 2 <description>adapter sequences</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
5 </requirements> | 5 </requirements> |
6 <command> | 6 <command> |
7 zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS | 7 <![CDATA[ |
8 zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS | |
8 #if $input.ext == "fastqsanger": | 9 #if $input.ext == "fastqsanger": |
9 -Q 33 | 10 -Q 33 |
10 #end if | 11 #end if |
11 </command> | 12 ]]> |
12 | 13 </command> |
13 <inputs> | |
14 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> | |
15 | |
16 <param name="minlength" size="4" type="integer" value="15"> | |
17 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> | |
18 </param> | |
19 | 14 |
20 <conditional name="clip_source"> | 15 <inputs> |
21 <param name="clip_source_list" type="select" label="Source"> | 16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> |
22 <option value="prebuilt" selected="true">Standard (select from the list below)</option> | |
23 <option value="user">Enter custom sequence</option> | |
24 </param> | |
25 | 17 |
26 <when value="user"> | 18 <param name="minlength" type="integer" value="15"> |
27 <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" /> | 19 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> |
28 </when> | 20 </param> |
29 | 21 |
30 <when value="prebuilt"> | 22 <conditional name="clip_source"> |
31 <param name="clip_sequence" type="select" label="Choose Adapter"> | 23 <param name="clip_source_list" type="select" label="Source"> |
32 <options from_file="fastx_clipper_sequences.txt"> | 24 <option value="prebuilt" selected="true">Standard (select from the list below)</option> |
33 <column name="name" index="1"/> | 25 <option value="user">Enter custom sequence</option> |
34 <column name="value" index="0"/> | 26 </param> |
35 </options> | |
36 </param> | |
37 </when> | |
38 </conditional> | |
39 | 27 |
40 <param name="keepdelta" size="2" type="integer" value="0"> | 28 <when value="user"> |
41 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> | 29 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" /> |
42 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> | 30 </when> |
43 </param> | |
44 | 31 |
45 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> | 32 <when value="prebuilt"> |
46 <option value="">Yes</option> | 33 <param name="clip_sequence" type="select" label="Choose Adapter"> |
47 <option value="-n">No</option> | 34 <options from_file="fastx_clipper_sequences.txt"> |
48 </param> | 35 <column name="name" index="1"/> |
36 <column name="value" index="0"/> | |
37 </options> | |
38 </param> | |
39 </when> | |
40 </conditional> | |
49 | 41 |
50 <param name="DISCARD_OPTIONS" type="select" label="Output options"> | 42 <param name="keepdelta" type="integer" value="0"> |
51 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> | 43 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> |
52 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> | 44 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> |
53 <option value="">Output both clipped and non-clipped sequences</option> | 45 </param> |
54 </param> | |
55 | 46 |
56 </inputs> | 47 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> |
57 <!-- | 48 <option value="">Yes</option> |
58 #functional test with param value starting with - fails. | 49 <option value="-n">No</option> |
59 --> | 50 </param> |
60 <tests> | 51 |
61 <test> | 52 <param name="DISCARD_OPTIONS" type="select" label="Output options"> |
62 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/> | 53 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> |
63 <param name="maxmismatches" value="2" /> | 54 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> |
64 <param name="minlength" value="15" /> | 55 <option value="">Output both clipped and non-clipped sequences</option> |
65 <param name="clip_source_list" value="user" /> | 56 </param> |
66 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> | 57 </inputs> |
67 <param name="keepdelta" value="0" /> | 58 <outputs> |
68 <param name="KEEP_N" value="+-n" /> | 59 <data format_source="input" name="output" metadata_source="input" /> |
69 <param name="DISCARD_OPTIONS" value="+-c" /> | 60 </outputs> |
70 <output name="output" file="fastx_clipper1a.out" /> | 61 <tests> |
71 </test> | 62 <test> |
72 </tests> | 63 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/> |
73 <outputs> | 64 <param name="maxmismatches" value="2" /> |
74 <data format="input" name="output" metadata_source="input" /> | 65 <param name="minlength" value="15" /> |
75 </outputs> | 66 <param name="clip_source_list" value="user" /> |
76 | 67 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> |
77 <help> | 68 <param name="keepdelta" value="0" /> |
69 <param name="KEEP_N" value="-n" /> | |
70 <param name="DISCARD_OPTIONS" value="-c" /> | |
71 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" /> | |
72 </test> | |
73 </tests> | |
74 <help> | |
78 **What it does** | 75 **What it does** |
79 | 76 |
80 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. | 77 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. |
81 | 78 |
82 -------- | 79 -------- |
83 | 80 |
84 | 81 |
85 **Clipping Illustration:** | 82 **Clipping Illustration:** |
86 | 83 |
87 .. image:: fastx_clipper_illustration.png | 84 .. image:: fastx_clipper_illustration.png |
88 | |
89 | |
90 | |
91 | |
92 | |
93 | |
94 | |
95 | 85 |
96 **Clipping Example:** | 86 **Clipping Example:** |
97 | 87 |
98 .. image:: fastx_clipper_example.png | 88 .. image:: fastx_clipper_example.png |
99 | 89 |
100 | |
101 | |
102 **In the above example:** | 90 **In the above example:** |
103 | 91 |
104 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). | 92 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). |
105 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). | 93 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). |
106 | |
107 | |
108 | |
109 | 94 |
110 ------ | 95 ------ |
111 | 96 |
112 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 97 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
113 | 98 |
114 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 99 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
115 | 100 </help> |
116 </help> | |
117 </tool> | 101 </tool> |