Mercurial > repos > peterjc > seq_primer_clip
comparison tools/seq_primer_clip/seq_primer_clip.xml @ 4:9b074c1db68e draft
v0.0.14 galaxy_sequence_utils dependency etc
author | peterjc |
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date | Thu, 02 Feb 2017 11:52:37 -0500 |
parents | ee5acea162a7 |
children | 530c8d6fedd8 |
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3:708ce1e5ac94 | 4:9b074c1db68e |
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1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10"> | 1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14"> |
2 <description>Trim off 5' or 3' primers</description> | 2 <description>Trim off 5' or 3' primers</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.62">biopython</requirement> | 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
5 <requirement type="package" version="1.67">biopython</requirement> | |
5 <requirement type="python-module">Bio</requirement> | 6 <requirement type="python-module">Bio</requirement> |
6 </requirements> | 7 </requirements> |
7 <version_command interpreter="python">seq_primer_clip.py --version</version_command> | |
8 <command interpreter="python"> | |
9 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | |
10 </command> | |
11 <stdio> | 8 <stdio> |
12 <!-- Anything other than zero is an error --> | 9 <!-- Anything other than zero is an error --> |
13 <exit_code range="1:" /> | 10 <exit_code range="1:" /> |
14 <exit_code range=":-1" /> | 11 <exit_code range=":-1" /> |
15 </stdio> | 12 </stdio> |
13 <version_command interpreter="python">seq_primer_clip.py --version</version_command> | |
14 <command interpreter="python"> | |
15 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | |
16 </command> | |
16 <inputs> | 17 <inputs> |
17 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/> | 18 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/> |
18 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> | 19 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> |
19 <param name="primer_type" type="select" label="Type of primers"> | 20 <param name="primer_type" type="select" label="Type of primers"> |
20 <option value="Forward">Forward (5') primers</option> | 21 <option value="Forward">Forward (5') primers</option> |
21 <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> | 22 <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> |
22 <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> | 23 <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> |
26 </param> | 27 </param> |
27 <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> | 28 <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> |
28 <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> | 29 <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> |
29 </inputs> | 30 </inputs> |
30 <outputs> | 31 <outputs> |
31 <data name="output_file" format="data" label="$primer_type primer clipped"> | 32 <data name="output_file" format_source="input_file" metadata_source="input_file" label="$primer_type primer clipped"/> |
32 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
33 <change_format> | |
34 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
35 <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" /> | |
36 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
37 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
38 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
39 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
40 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
41 </change_format> | |
42 </data> | |
43 </outputs> | 33 </outputs> |
44 <tests> | 34 <tests> |
45 <test> | 35 <test> |
46 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> | 36 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> |
47 <param name="primer_fasta" value="dop_primers.fasta" /> | 37 <param name="primer_fasta" value="dop_primers.fasta" /> |
95 <param name="keep_negatives" value="true" /> | 85 <param name="keep_negatives" value="true" /> |
96 <param name="min_len" value="35" /> | 86 <param name="min_len" value="35" /> |
97 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | 87 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> |
98 </test> | 88 </test> |
99 </tests> | 89 </tests> |
100 <requirements> | |
101 <requirement type="python-module">Bio</requirement> | |
102 </requirements> | |
103 <help> | 90 <help> |
104 | 91 |
105 **What it does** | 92 **What it does** |
106 | 93 |
107 Looks for the given primer sequences (within the existing clipped sequence) and | 94 Looks for the given primer sequences (within the existing clipped sequence) and |
138 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | 125 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
139 | 126 |
140 This tool is available to install into other Galaxy Instances via the Galaxy | 127 This tool is available to install into other Galaxy Instances via the Galaxy |
141 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip | 128 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip |
142 </help> | 129 </help> |
130 <citations> | |
131 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
132 </citations> | |
143 </tool> | 133 </tool> |