diff spotyping.xml @ 0:7412632c7b0e draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spotyping.xml	Tue Nov 13 10:46:18 2018 -0500
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+<tool id="spotyping" name="Spoligotype Prediction" version="1.0.4">
+    <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
+    <requirements>
+        <requirement type="package" version="2.1">spotyping</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        SpoTyping.py
+        $advanced.seq
+        $advanced.swift
+        --min=$advanced.min
+        --rmin=$advanced.min_relax
+        #if str( $data_input.data_selector ) == "paired"       
+            $data_input.input1.forward $data_input.input1.reverse
+        #end if
+        #if str( $data_input.data_selector ) == "single"       
+            $data_input.input2
+        #end if
+        && cp SITVIT_ONLINE.*.xls spotyping.xls
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="data_input">
+            <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
+            </when>
+            <when value="single">
+                <param name="input2" format="data" type="data_collection" label="input" help="Specify dataset with single reads"/>
+            </when>
+        </conditional>
+        <section name="advanced" title="Advanced options" expanded="false">
+            <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 name="min" type="integer" value="5" label="MIN" help="minimum number of error-free hits to support presence of a spacer" />
+            <param name="min_relax" type="integer" value="6" label="MIN RELAX" help="minimum number of 1-error-tolerant hits to support presence of a spacer " />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="spotyping_results" label="spoligotyping results" format="txt" from_work_dir="SpoTyping"/>
+        <data name="spotyping_log" label="spoligotyping log" format="txt" from_work_dir="SpoTyping.log"/>
+        <data name="sitvit_database_query" label="query" format="excel.xls" from_work_dir="spotyping.xls"/>
+    </outputs>
+    <help><![CDATA[
+This is a modified version of IUC's wrapper of spotyping without the concatenation and renaming of the input files. The wrapper also runs properly when supplied with paired-end reads
+
+            SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
+
+    **Input:**
+
+    - 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)
+    - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
+
+    *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
+    paired end sequencing of a *M. tuberculosis* genome.
+
+    **Output:**
+
+    Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
+
+    **Options:**
+
+
+    \--seq
+    Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
+
+    \-s SWIFT, --swift=SWIFT
+    Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
+
+    \-m MIN, --min=MIN
+    minimum number of error-free hits to support presence of a spacer [Default: 5]
+    
+    \-r MIN_RELAX, --rmin=MIN_RELAX
+    minimum number of 1-error-tolerant hits to support presence of a spacer [Default: 6].
+
+
+
+    **Got weird spoligotype prediction?**
+
+    Sequencing throughput is very low (<40Mbp, for example): SpoTyping may not be able to give accurate prediction due to the relatively low read depth.
+
+    **Interpreting the spoligotype**
+
+    The binary or octal spoligotype can be used to look up lineage information using a service
+    like `TB Lineage`_.
+
+    **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="bibtex">
+@misc{githubSpoTyping,
+  author = {Xia, Eryu},
+  year = {2016},
+  title = {SpoTyping},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/xiaeryu/SpoTyping},
+}</citation>
+        <citation type="doi">10.1186/s13073-016-0270-7</citation>
+    </citations>
+</tool>