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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
author iuc
date Sat, 06 Oct 2018 18:48:35 -0400
parents 545d934aed81
children efa2be6db310
comparison
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0:545d934aed81 1:f82981245fbe
1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy0" profile="17.01"> 1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01">
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description> 2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
3 3
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">2.1</token> 5 <import>spotyping_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
10 </requirements> 10 </requirements>
11 11
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #set $input_file='input.' + $input.extension 13 #set $input_file='input.' + $input.extension
14 ln -s '${input}' $input_file && 14 ln -s '${input}' $input_file &&
15 SpoTyping.py 15 SpoTyping.py
16 --noQuery 16 $advanced.noQuery
17 $advanced.seq 17 $advanced.seq
18 $advanced.swift 18 $advanced.swift
19 $advanced.filter 19 $advanced.filter
20 $advanced.sorted 20 $advanced.sorted
21 $input_file && 21 $input_file &&
22 cat SpoTyping.log SpoTyping > '${output_txt}' 22 cat SpoTyping.log SpoTyping > '${output_txt}'
23 #if $advanced.noQuery != '--noQuery':
24 && cp SITVIT_ONLINE.*.xls '${output_xls}'
25 #if $advanced.pdf_plot == 'yes':
26 && SpoTyping_plot.r '${output_xls}' '${output_pdf}'
27 #end if
28 #end if
23 ]]> 29 ]]>
24 </command> 30 </command>
25 31
26 <inputs> 32 <inputs>
27 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" /> 33 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
28 <section name="advanced" title="Advanced options" expanded="false"> 34 <section name="advanced" title="Advanced options" expanded="false">
35 <param type="boolean" argument="--noQuery" label="Query SITVIT" truevalue="" falsevalue="--noQuery" checked="false" help="Query SITVIT service for report on spoligotype" />
29 <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" /> 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" />
30 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" /> 37 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
31 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" /> 38 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
32 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" /> 39 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
40 <param type="boolean" name="pdf_plot" label="Generate plot from SITVIT report output" truevalue="yes" falsevalue="" />
33 </section> 41 </section>
34 </inputs> 42 </inputs>
35 43
36 <outputs> 44 <outputs>
37 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" /> 45 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
46 <data name="output_xls" label="SpoTyping SITVIT report on ${on_string}" format="excel.xls">
47 <filter>advanced['noQuery']</filter>
48 </data>
49 <data name="output_pdf" label="SpoTyping plot from SITVIT report on ${on_string}" format="pdf">
50 <filter>advanced['pdf_plot']</filter>
51 </data>
38 </outputs> 52 </outputs>
39 53
40 <tests> 54 <tests>
41 <test> 55 <test expect_num_outputs="1">
42 <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> 56 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
43 <output name="output_txt"> 57 <output name="output_txt">
44 <assert_contents> 58 <assert_contents>
45 <has_text text="1111111111111111101111111111111100001111111" /> 59 <has_text text="1111111111111111101111111111111100001111111" />
46 </assert_contents> 60 </assert_contents>
47 </output> 61 </output>
48 </test> 62 </test>
63 <test expect_num_outputs="2">
64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
65 <param name="noQuery" value="" />
66 <output name="output_txt">
67 <assert_contents>
68 <has_text text="1111111111111111101111111111111100001111111" />
69 </assert_contents>
70 </output>
71 <output name="output_xls">
72 <assert_contents>
73 <has_text text="Spoligotype" />
74 </assert_contents>
75 </output>
76 </test>
77 <test expect_num_outputs="3">
78 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
79 <param name="noQuery" value="" />
80 <param name="pdf_plot" value="yes" />
81 <output name="output_txt">
82 <assert_contents>
83 <has_text text="1111111111111111101111111111111100001111111" />
84 </assert_contents>
85 </output>
86 <output name="output_xls">
87 <assert_contents>
88 <has_text text="Spoligotype" />
89 </assert_contents>
90 </output>
91 <output name="output_pdf">
92 <assert_contents>
93 <has_text text="PDF-1.4" />
94 </assert_contents>
95 </output>
96 </test>
97
49 </tests> 98 </tests>
50 99
51 <help><![CDATA[ 100 <help><![CDATA[
52 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs. 101 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
53 102
62 **Output:** 111 **Output:**
63 112
64 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code. 113 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
65 114
66 **Options:** 115 **Options:**
116
117 \--noQuery
118 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
67 119
68 \--seq 120 \--seq
69 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off] 121 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
70 122
71 \-s SWIFT, --swift=SWIFT 123 \-s SWIFT, --swift=SWIFT
90 **Interpreting the spoligotype** 142 **Interpreting the spoligotype**
91 143
92 The binary or octal spoligotype can be used to look up lineage information using a service 144 The binary or octal spoligotype can be used to look up lineage information using a service
93 like `TB Lineage`_. 145 like `TB Lineage`_.
94 146
95 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine 147 **SITVIT reports**
148
149 Optionally a report on the detected spoligotype can be retrieved from the SITVIT_ database. If such a report is requested it can also be
150 illustrated as a (PDF format) plot.
151
152 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
96 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871 153 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
97 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html 154 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
155 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
98 ]]> 156 ]]>
99 </help> 157 </help>
100 158
101 <citations> 159 <citations>
102 <citation type="doi">10.1186/s13073-016-0270-7</citation> 160 <expand macro="spotyping_citation" />
103 </citations> 161 </citations>
104 </tool> 162 </tool>