diff interproscan.xml @ 0:59d780043157 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interproscan.xml	Tue Apr 03 14:30:53 2018 -0400
@@ -0,0 +1,84 @@
+<tool id="statonlab_interproscan" name="statonlab interproscan" version="1.0.0">
+    <description>search nucleotide and protein sequences</description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
+
+Rscript '${__tool_directory__}/'interproscan_render.R
+
+	-o '$report'
+	-d '$report.files_path'
+	-s '$sink_message'
+	-A '$fasta_input'
+	-B '$output_format'
+	-C '$disable_precalc'
+	-D '$iprlookup'
+	-E '$goterms'
+	-F '$pathways'
+]]></command>
+    <inputs>
+        <param type="data" name="fasta_input" label="sequences in fasta format" optional="False" format="fasta,fa"/>
+        <param type="select" name="output_format" argument="-f" label="Output format" optional="False" multiple="True">
+            <option value="TSV" selected="false">TSV</option>
+            <option value="XML" selected="false">XML</option>
+            <option value="JSON" selected="false">JSON</option>
+            <option value="GFF3" selected="false">GFF3</option>
+            <option value="HTML" selected="false">HTML</option>
+            <option value="SVG" selected="false">SVG</option>
+        </param>
+        <param type="boolean" name="disble_precalc" argument="--disable-precalc" label="disable precalc"
+               help="Disables use of the precalculated match lookup service" optional="False" checked="True"
+               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
+        <param type="boolean" name="iprlookup" argument="--iprlookup" label="lookup corresponding InterPro annotation"
+               help="Also include lookup of corresponding InterPro annotation in the TSV and GFF3 output formats"
+               optional="False" checked="True" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
+        <param type="boolean" name="goterms" argument="--goterms"
+               label="switch on lookup of corresponding Gene Ontology" optional="False" checked="True"
+               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
+        <param type="boolean" name="pathways" argument="--pathways"
+               label="switch on lookup of corresponding Pathway annotation" optional="False" checked="True"
+               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="tool report"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
+    </outputs>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[@article{jones2014interproscan,
+  title={InterProScan 5: genome-scale protein function classification},
+  author={Jones, Philip and Binns, David and Chang, Hsin-Yu and Fraser, Matthew and Li, Weizhong and McAnulla, Craig and McWilliam, Hamish and Maslen, John and Mitchell, Alex and Nuka, Gift and others},
+  journal={Bioinformatics},
+  volume={30},
+  number={9},
+  pages={1236--1240},
+  year={2014},
+  publisher={Oxford University Press}
+}]]></citation>
+    </citations>
+</tool>