Mercurial > repos > iuc > spotyping

annotate spotyping.xml @ 2:0061b5818bb5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
author iuc
date Sun, 21 Oct 2018 13:02:43 -0400
parents ee9f908ce860
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy2" profile="17.01">
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
3
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
4 <macros>
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
5 <import>spotyping_macros.xml</import>
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
6 </macros>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
7
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
8 <requirements>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
10 </requirements>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
11
2
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
13 #set $input_file='input.' + $input.extension
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
14 ln -s '${input}' $input_file &&
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
15 SpoTyping.py
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
16 $advanced.noQuery
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
17 $advanced.seq
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
18 $advanced.swift
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
19 $advanced.filter
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
20 $advanced.sorted
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
21 $input_file &&
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
22 cat SpoTyping.log SpoTyping > '${output_txt}'
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
23 #if $advanced.noQuery != '--noQuery':
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
24 && cp SITVIT_ONLINE.*.xls '${output_xls}'
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
25 #if $advanced.pdf_plot == 'yes':
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
26 && SpoTyping_plot.r '${output_xls}' '${output_pdf}'
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
27 #end if
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
28 #end if
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
29 ]]>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
30 </command>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
31
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
32 <inputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
33 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
34 <section name="advanced" title="Advanced options" expanded="false">
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
35 <param type="boolean" argument="--noQuery" label="Query SITVIT" truevalue="" falsevalue="--noQuery" checked="false" help="Query SITVIT service for report on spoligotype" />
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
36 <param type="boolean" argument="--seq" label="Input is assembled sequence" help="Input is either a complete genomic sequence or assembled contigs from an isolate" truevalue="--seq" falsevalue="" checked="false" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
37 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
38 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
39 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
40 <param type="boolean" name="pdf_plot" label="Generate plot from SITVIT report output" truevalue="yes" falsevalue="" />
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
41 </section>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
42 </inputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
43
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
44 <outputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
45 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
46 <data name="output_xls" label="SpoTyping SITVIT report on ${on_string}" format="excel.xls">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
47 <filter>advanced['noQuery']</filter>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
48 </data>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
49 <data name="output_pdf" label="SpoTyping plot from SITVIT report on ${on_string}" format="pdf">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
50 <filter>advanced['pdf_plot']</filter>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
51 </data>
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
52 </outputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
53
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
54 <tests>
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
55 <test expect_num_outputs="1">
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
56 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
57 <output name="output_txt">
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
58 <assert_contents>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
59 <has_text text="1111111111111111101111111111111100001111111" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
60 </assert_contents>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
61 </output>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
62 </test>
2
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
63 <test expect_failure="true">
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
65 <param name="seq" value="--seq" />
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
66 <assert_stderr>
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
67 <has_text text="BLAST options error" />
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
68 </assert_stderr>
0061b5818bb5 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
iuc
parents: 1
diff changeset
69 </test>
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
70 <test expect_num_outputs="2">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
71 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
72 <param name="noQuery" value="" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
73 <output name="output_txt">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
74 <assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
75 <has_text text="1111111111111111101111111111111100001111111" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
76 </assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
77 </output>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
78 <output name="output_xls">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
79 <assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
80 <has_text text="Spoligotype" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
81 </assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
82 </output>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
83 </test>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
84 <test expect_num_outputs="3">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
85 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
86 <param name="noQuery" value="" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
87 <param name="pdf_plot" value="yes" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
88 <output name="output_txt">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
89 <assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
90 <has_text text="1111111111111111101111111111111100001111111" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
91 </assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
92 </output>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
93 <output name="output_xls">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
94 <assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
95 <has_text text="Spoligotype" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
96 </assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
97 </output>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
98 <output name="output_pdf">
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
99 <assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
100 <has_text text="PDF-1.4" />
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
101 </assert_contents>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
102 </output>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
103 </test>
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
104
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
105 </tests>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
106
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
107 <help><![CDATA[
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
108 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
109
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
110 **Input:**
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
111
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
112 - Fastq file - if paired end data is used, you may choose to concatenate paired reads into a single input (e.g. using the cat tool)
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
113 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
114
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
115 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
116 paired end sequencing of a *M. tuberculosis* genome.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
117
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
118 **Output:**
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
119
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
120 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
121
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
122 **Options:**
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
123
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
124 \--noQuery
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
125 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
126
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
127 \--seq
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
128 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
129
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
130 \-s SWIFT, --swift=SWIFT
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
131 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
132
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
133 \--sorted
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
134 Set if input reads are sorted relative to positions on a reference genome. If reads are sorted and swift mode is used, swift mode's sampling is adjusted
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
135 to sample reads across positions in the genome evenly.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
136
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
137 \--filter
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
138 Filter reads such that:
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
139
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
140 1. Leading and trailing 'N's would be removed.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
141 2. Any read with more than 3 'N's in the middle would be removed.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
142 3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
143 the length of the flanking regions.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
144
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
145 **Got weird spoligotype prediction?**
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
146
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
147 Sequencing throughput is very low (<40Mbp, for example): SpoTyping may not be able to give accurate prediction due to the relatively low read depth.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
148
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
149 **Interpreting the spoligotype**
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
150
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
151 The binary or octal spoligotype can be used to look up lineage information using a service
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
152 like `TB Lineage`_.
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
153
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
154 **SITVIT reports**
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
155
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
156 Optionally a report on the detected spoligotype can be retrieved from the SITVIT_ database. If such a report is requested it can also be
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
157 illustrated as a (PDF format) plot.
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
158
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
159 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
160 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
161 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
162 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
163 ]]>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
164 </help>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
165
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
166 <citations>
1
ee9f908ce860 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
diff changeset
167 <expand macro="spotyping_citation" />
0
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
168 </citations>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
parents:
diff changeset
169 </tool>