Mercurial > repos > iuc > spotyping
comparison spotyping.xml @ 1:f82981245fbe draft
planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
author | iuc |
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date | Sat, 06 Oct 2018 18:48:35 -0400 |
parents | 545d934aed81 |
children | efa2be6db310 |
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0:545d934aed81 | 1:f82981245fbe |
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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> |