diff split_fasta.xml @ 1:ecf34bd52987 draft

update

--- a/split_fasta.xml	Mon Apr 09 11:51:32 2018 -0400
+++ b/split_fasta.xml	Mon Apr 09 13:32:55 2018 -0400
@@ -1,17 +1,11 @@
 <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>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='${__tool_directory__}' &&
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="5.22.2.1">perl</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'split_fasta_render.R
 
@@ -21,19 +15,11 @@
 	-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 ${on_string}">
-            <discover_datasets pattern="__name_and_ext__" directory="fasta_files" visible="true"/>
-        </collection>
-    </outputs>
-    <citations>
+  <inputs>
+    <param type="data" name="fasta_input" label="FASTA input" optional="False" multiple="False"/><param type="integer" name="number" label="Number" help="The number of files the FASTA file will be split into" optional="False" value="200" min="1"/></inputs>
+  <outputs>
+        <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/><data name="sink_message" format="txt" label="${tool.name} log on ${on_string}" from_work_dir="warnings_and_errors.txt" hidden="false"/><collection name="list_collection" type="list" label="${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},
@@ -43,8 +29,7 @@
             volume={6},
             year={2016}
             }
-        ]]></citation>
-        <citation type="bibtex"><![CDATA[
+        ]]></citation><citation type="bibtex"><![CDATA[
             @book{xie2015dynamic,
             title={Dynamic Documents with R and knitr},
             author={Xie, Yihui},
@@ -52,6 +37,5 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-    </citations>
+        ]]></citation></citations>
 </tool>