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comparison filter-stats.xml @ 0:89c3ba37711c draft

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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author nml
date Tue, 27 Aug 2019 12:31:08 -0400
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1 <tool id="filterstat" name="Filter Stats" version ="1.8.2">
2 <description>Identify number of positions excluded based on filtered status</description>
3 <requirements>
4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 filter-stats.pl -i $tabfile
8 #if $summary:
9 -a
10 #end if
11 > $out
12 </command>
13 <inputs>
14 <param name="tabfile" type="data" label="SNV-alignment positions tab delimited file" format="tabular"/>
15 <param name="summary" type="select" display="checkboxes" label="Summary Options" multiple="true">
16 <option value="invalids">Include all entries marked as 'filtered-invalid'</option>
17 </param>
18 </inputs>
19 <outputs>
20 <data format="tabular" name="out" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="tabfile" value="filter-stats-in.tsv" />
25 <output name="out" file="filter-stats-out.tabular" />
26 </test>
27 </tests>
28
29 <help>
30 What it does
31 ============
32
33 This script prints a stat summary of the number of N's and -'s found in the SNV-alignment positions tab delimited file.
34
35
36 Usage
37 =====
38
39 **Parameters**
40 - input - The SNV-alignment positions tab delimited file
41
42
43 **Options**
44 - -all When this option is set, the summary will include all the entries marked as 'filtered-invalid'
45 </help>
46 <citations>
47 </citations>
48 </tool>