diff split_fasta.xml @ 0:3918528c19b4 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_fasta.xml	Mon Apr 09 11:51:32 2018 -0400
@@ -0,0 +1,57 @@
+<tool id="statonlab_fasta_splitter" name="statonlab_fasta_splitter" version="1.0.0">
+    <description>Split a single FASTA file into multiple smaller FASTA files&#xD;
+    </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>
+        <requirement type="package" version="5.22.2.1">perl</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__}/'split_fasta_render.R
+
+	-o '$report'
+	-d '$report.files_path'
+	-s '$sink_message'
+	-A '$fasta_input'
+	-B '$number'
+]]></command>
+    <inputs>
+        <param type="data" name="fasta_input" label="FASTA input" optional="False" multiple="False"/>
+        <param type="integer" name="number" label="Number" help="The number of files the FASTA file will be split into"
+               optional="False" value="200" min="1"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="tool report"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
+        <collection name="list_collection" type="list" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__name_and_ext__" directory="fasta_files" visible="true"/>
+        </collection>
+    </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>
+    </citations>
+</tool>