Mercurial > repos > geert-vandeweyer > multiplicom_primer_trimming
comparison multiplicom_primer_trimming.xml @ 0:fadef644b886 draft
Uploaded
author | geert-vandeweyer |
---|---|
date | Fri, 22 May 2015 08:27:03 -0400 |
parents | |
children | b2125910c8fd |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:fadef644b886 |
---|---|
1 <tool id="multiplicom_primer_trimming" name="Multiplicom Primer Trimmer" version="0.0.1"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version='latest'>twoBitToFa</requirement> | |
5 </requirements> | |
6 <command interpreter="perl"> | |
7 multiplicom_primer_trimming.pl | |
8 ## input files | |
9 -i $inputf | |
10 -I $inputr | |
11 -b $mastr | |
12 ## read length | |
13 -r $readlength | |
14 ## output files | |
15 -o $outf | |
16 -O $outr | |
17 -F $failed | |
18 -R $report | |
19 ## reference genome | |
20 -t "${indexes.fields.path}" | |
21 | |
22 </command> | |
23 <inputs> | |
24 <param name='inputf' type='data' format='fastq,fastqsanger' label='Forward Sequences' help='Forward Reads in fastq format' /> | |
25 <param name='inputr' type='data' format='fastq,fastqsanger' label='Reverse Sequences' help='Reverse Reads in fastq format' /> | |
26 <param name='mastr' type='data' format='bed' label='MASTR file' help='Design file of the Multiplicom MASTR assay' /> | |
27 <param name='readlength' type='integer' value='250' label='Read Length' help='Applied Readlength, per read' /> | |
28 <param name="indexes" type="select" label="Reference Genome" help="Select the correct genome build" > | |
29 <options from_data_table="twobit" > | |
30 <filter type="sort_by" column="2" /> | |
31 <validator type="no_options" message="No indexes are available" /> | |
32 </options> | |
33 </param> | |
34 </inputs> | |
35 <outputs> | |
36 <data format_source="inputf" name="outf" label="${tool.name} on ${on_string}: Forward Reads"/> | |
37 <data format_source="inputr" name="outr" label="${tool.name} on ${on_string}: Reverse Reads"/> | |
38 <data format_source="inputf" name="failed" label="${tool.name} on ${on_string}: Failed Pairs"/> | |
39 <data format="txt" name="report" label="${tool.name} on ${on_string}: Runtime output"/> | |
40 </outputs> | |
41 <help> | |
42 This tools scans paired FASTQ files for the presence of Multiplicom MASTR PCR primers. If found, primers are clipped. | |
43 </help> | |
44 </tool> | |
45 |