Mercurial > repos > mingchen0919 > aurora_skewer_site

changeset 1:0483f55131d1 draft

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update name
author mingchen0919
date Fri, 02 Mar 2018 10:23:17 -0500
parents ad0aa8d214c1
children 8f06a3c1e83b
files skewer.xml
diffstat 1 files changed, 23 insertions(+), 51 deletions(-) [+]
line wrap: on
line diff
--- a/skewer.xml	Fri Mar 02 10:20:53 2018 -0500
+++ b/skewer.xml	Fri Mar 02 10:23:17 2018 -0500
@@ -1,17 +1,11 @@
-<tool id="aurora_skewer" name="Aurora Skewer" version="1.0.0">
-    <description>A fast and accurate adapter trimmer for next-generation sequencing paired-end reads&#xD;
+<tool id="aurora_skewer_site" name="Aurora Skewer Site" version="1.0.0">
+  <description>A fast and accurate adapter trimmer for next-generation sequencing paired-end reads&#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="0.2.2">skewer</requirement>
-    </requirements>
-    <stdio>
-        <regex match="XXX" source="stderr" level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command><![CDATA[Rscript '${__tool_directory__}/skewer_render.R'
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="0.2.2">skewer</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[Rscript '${__tool_directory__}/skewer_render.R'
 
     -e $echo
     -o $report
@@ -29,30 +23,11 @@
     -f $trimmed_r1
     -r $trimmed_r2
 ]]></command>
-    <inputs>
-        <param type="data" name="first_reads" label="First reads file" optional="False" format="fastq,fastqsanger"/>
-        <param type="data" name="second_reads" label="Second reads" optional="False" format="fastq,fastqsanger"/>
-        <param type="data" name="adapter_x" argument="-x" label="Adapter sequence file for the first reads"
-               optional="True" format="fasta,fa"/>
-        <param type="data" name="adapter_y" argument="-y" label="Adapter sequence file for the second reads"
-               optional="True" format="fasta,fa"/>
-        <param type="integer" name="end_quality" argument="-q" label="3&#x2019; end quality trimming"
-               help="Trim 3&#x2019; end until specified or higher quality reached. The default value is 0."
-               optional="False" value="0"/>
-        <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
-               help="Specifies the lowest mean quality value allowed before trimming. The default value is 0."
-               optional="False" value="0"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
-               label="Display analysis code in report?"/>
-    </inputs>
-    <outputs>
-        <data name="report" format="html" label="Skewer trimmed" hidden="false"/>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
-        <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
-        <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
-              hidden="false"/>
-    </outputs>
-    <citations>
+  <inputs>
+        <param type="data" name="first_reads" label="First reads file" optional="False" format="fastq,fastqsanger"/><param type="data" name="second_reads" label="Second reads" optional="False" format="fastq,fastqsanger"/><param type="data" name="adapter_x" argument="-x" label="Adapter sequence file for the first reads" optional="True" format="fasta,fa"/><param type="data" name="adapter_y" argument="-y" label="Adapter sequence file for the second reads" optional="True" format="fasta,fa"/><param type="integer" name="end_quality" argument="-q" label="3&#x2019; end quality trimming" help="Trim 3&#x2019; end until specified or higher quality reached. The default value is 0." optional="False" value="0"/><param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality" help="Specifies the lowest mean quality value allowed before trimming. The default value is 0." optional="False" value="0"/><param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/></inputs>
+  <outputs>
+        <data name="report" format="html" label="Skewer trimmed" hidden="false"/><data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/><data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/><data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}" hidden="false"/></outputs>
+  <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
@@ -62,8 +37,7 @@
             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},
@@ -71,16 +45,14 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-        <citation type="bibtex"><![CDATA[@article{jiang2014skewer,
-  title={Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads},
-  author={Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang},
-  journal={BMC bioinformatics},
-  volume={15},
-  number={1},
-  pages={182},
-  year={2014},
-  publisher={BioMed Central}
-}]]></citation>
-    </citations>
+        ]]></citation><citation type="bibtex"><![CDATA[@article{jiang2014skewer,
+  title={Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads},
+  author={Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang},
+  journal={BMC bioinformatics},
+  volume={15},
+  number={1},
+  pages={182},
+  year={2014},
+  publisher={BioMed Central}
+}]]></citation></citations>
 </tool>