Mercurial > repos > iuc > spotyping
changeset 1:f82981245fbe draft
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 |
| files | spotyping.xml spotyping_macros.xml test-data/input.sitvit.xls test-data/output.sitvit.pdf |
| diffstat | 4 files changed, 70 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/spotyping.xml Tue May 08 10:22:03 2018 -0400 +++ b/spotyping.xml Sat Oct 06 18:48:35 2018 -0400 @@ -1,8 +1,8 @@ -<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy0" profile="17.01"> +<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01"> <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description> <macros> - <token name="@TOOL_VERSION@">2.1</token> + <import>spotyping_macros.xml</import> </macros> <requirements> @@ -13,32 +13,46 @@ #set $input_file='input.' + $input.extension ln -s '${input}' $input_file && SpoTyping.py - --noQuery + $advanced.noQuery $advanced.seq $advanced.swift $advanced.filter $advanced.sorted $input_file && cat SpoTyping.log SpoTyping > '${output_txt}' + #if $advanced.noQuery != '--noQuery': + && cp SITVIT_ONLINE.*.xls '${output_xls}' + #if $advanced.pdf_plot == 'yes': + && SpoTyping_plot.r '${output_xls}' '${output_pdf}' + #end if + #end if ]]> </command> <inputs> <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" /> <section name="advanced" title="Advanced options" expanded="false"> + <param type="boolean" argument="--noQuery" label="Query SITVIT" truevalue="" falsevalue="--noQuery" checked="false" help="Query SITVIT service for report on spoligotype" /> <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" /> <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" /> <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" /> <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" /> + <param type="boolean" name="pdf_plot" label="Generate plot from SITVIT report output" truevalue="yes" falsevalue="" /> </section> </inputs> <outputs> <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" /> + <data name="output_xls" label="SpoTyping SITVIT report on ${on_string}" format="excel.xls"> + <filter>advanced['noQuery']</filter> + </data> + <data name="output_pdf" label="SpoTyping plot from SITVIT report on ${on_string}" format="pdf"> + <filter>advanced['pdf_plot']</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> <output name="output_txt"> <assert_contents> @@ -46,6 +60,41 @@ </assert_contents> </output> </test> + <test expect_num_outputs="2"> + <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> + <param name="noQuery" value="" /> + <output name="output_txt"> + <assert_contents> + <has_text text="1111111111111111101111111111111100001111111" /> + </assert_contents> + </output> + <output name="output_xls"> + <assert_contents> + <has_text text="Spoligotype" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> + <param name="noQuery" value="" /> + <param name="pdf_plot" value="yes" /> + <output name="output_txt"> + <assert_contents> + <has_text text="1111111111111111101111111111111100001111111" /> + </assert_contents> + </output> + <output name="output_xls"> + <assert_contents> + <has_text text="Spoligotype" /> + </assert_contents> + </output> + <output name="output_pdf"> + <assert_contents> + <has_text text="PDF-1.4" /> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ @@ -65,6 +114,9 @@ **Options:** + \--noQuery + Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype. + \--seq Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off] @@ -92,13 +144,19 @@ The binary or octal spoligotype can be used to look up lineage information using a service like `TB Lineage`_. - .. _SpoTyping: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine + **SITVIT reports** + + Optionally a report on the detected spoligotype can be retrieved from the SITVIT_ database. If such a report is requested it can also be + illustrated as a (PDF format) plot. + + .. _SpoTyping: https://github.com/xiaeryu/SpoTyping .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html + .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/ ]]> </help> <citations> - <citation type="doi">10.1186/s13073-016-0270-7</citation> + <expand macro="spotyping_citation" /> </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spotyping_macros.xml Sat Oct 06 18:48:35 2018 -0400 @@ -0,0 +1,6 @@ +<macros> + <token name="@TOOL_VERSION@">2.1</token> + <xml name="spotyping_citation"> + <citation type="doi">10.1186/s13073-016-0270-7</citation> + </xml> +</macros> \ No newline at end of file