comparison tools/seq_primer_clip/seq_primer_clip.xml @ 4:9b074c1db68e draft

v0.0.14 galaxy_sequence_utils dependency etc
author peterjc
date Thu, 02 Feb 2017 11:52:37 -0500
parents ee5acea162a7
children 530c8d6fedd8
comparison
equal deleted inserted replaced
3:708ce1e5ac94 4:9b074c1db68e
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>