# HG changeset patch
# User mingchen0919
# Date 1521390558 14400
# Node ID 1731a1cca2260e51e8e65f83a10fea5cbb27b4bb
# Parent  d9601e1eb360c4519c9c24225373aef5f07660d1
v1.1.0

diff -r d9601e1eb360 -r 1731a1cca226 skewer.Rmd
--- a/skewer.Rmd	Sun Mar 18 11:07:16 2018 -0400
+++ b/skewer.Rmd	Sun Mar 18 12:29:18 2018 -0400
@@ -4,7 +4,6 @@
     html_document:
       number_sections: true
       highlight: tango
-      code_folding: hide
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
@@ -15,7 +14,7 @@
 ```
 
 
-# Run Skewer
+
 
 ```{bash echo=FALSE}
 #--- build skewer job script ---
@@ -56,10 +55,10 @@
   sed 's/NO_ARGUMENT_YES//g' > skewer-job.sh
 ```
 
-```{r echo=FALSE}
-# display skewer job script
-skewer_sh = paste0(opt$X_d, '/skewer-job.sh')
-tags$code(tags$pre(readChar(skewer_sh, file.info(skewer_sh)$size )))
+**Skewer job script: [skewer-job.sh](skewer-job.sh)**
+
+```bash
+  `r readChar(paste0(opt$X_d, '/skewer-job.sh'), file.info(paste0(opt$X_d, '/skewer-job.sh'))$size)`
 ```
 
 ```{bash echo=FALSE}
@@ -86,21 +85,23 @@
 ```
 
 
-
-# Results
+```{r echo=FALSE}
+checked_file = function(fastq) {
+  if(file.exists(paste0(opt$X_d, '/', fastq))) {
+    string = paste0('[', fastq, ']', '(', fastq, ')')
+  } else {
+    string = paste0(fastq, ' not available')
+  }
+  string
+}
+```
 
-```{r echo=FALSE}
-if (file.exists(paste0(opt$X_d, '/trim-trimmed.fastq'))) {
-  tags$ul(
-    tags$li(tags$a(href = 'trim-trimmed.txt', 'trim-trimmed.log')),
-    tags$li(tags$a(href = 'trim-trimmed.fastq', 'trim-trimmed.fastq'))
-  )
-} else {
-  tags$ul(
-    tags$li(tags$a(href = 'trim-trimmed.txt', 'trim-trimmed.log')),
-    tags$li(tags$a(href = 'trim-trimmed-pair1.fastq', 'trim-trimmed-pair1.fastq')),
-    tags$li(tags$a(href = 'trim-trimmed-pair2.fastq', 'trim-trimmed-pair2.fastq'))
-  )
-}
+**Results**
 
-```
+  * [Trimming log](trim-trimmed.txt)
+  * `r checked_file('trim-trimmed.fastq')`
+  * `r checked_file('trim-trimmed-pair1.fastq')`
+  * `r checked_file('trim-trimmed-pair2.fastq')`
+
+
+
diff -r d9601e1eb360 -r 1731a1cca226 skewer.xml
--- a/skewer.xml	Sun Mar 18 11:07:16 2018 -0400
+++ b/skewer.xml	Sun Mar 18 12:29:18 2018 -0400
@@ -1,17 +1,11 @@
-<tool id="tool_1" name="Aurora Skewer" version="1.1.0">
-    <description>A fast and accurate adapter trimmer for next-generation sequencing paired-end reads&#xD;
+<tool id="tool_1" name="Aurora Skewer" 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[export TOOL_DIR='${__tool_directory__}' &&
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="0.2.2">skewer</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
 
 Rscript '${__tool_directory__}/'skewer_render.R
 
@@ -43,84 +37,12 @@
 	-2 '$trimmed_r2'
 	-3 '$trimmed_s'
 ]]></command>
-    <inputs>
-        <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"
-               multiple="True"/>
-        <param type="data" name="second_reads" label="Second reads"
-               help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only."
-               optional="True" format="fastq,fastqsanger" multiple="True"/>
-        <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads."
-               optional="True" format="fasta,fa" multiple="False"/>
-        <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads"
-               optional="True" format="fasta,fa" multiple="False"/>
-        <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False">
-            <option value="None" selected="true">--select a model--</option>
-            <option value="head" selected="false">5&#x2019; end trimming (single end reads)</option>
-            <option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option>
-            <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option>
-            <option value="pe" selected="false">paired-end trimming</option>
-            <option value="mp" selected="false">mate-pair trimming</option>
-            <option value="ap" selected="false">amplicon trimming</option>
-        </param>
-        <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate"
-               optional="False" value="0.1" min="0" max="0.5"/>
-        <param type="float" name="maximum_allowed_indel_error_rate" argument="-d"
-               label="Maximum allowed indel error rate"
-               help="The valid range of indel error rate is [0,  maximum allowed error rate]" optional="False"
-               value="0.03" min="0"/>
-        <param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming"
-               optional="False" value="0"/>
-        <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
-               optional="False" value="0"/>
-        <param type="integer" name="minimum_read_length" argument="-l"
-               label="Minimum read length allowed after trimming" optional="False" value="18"/>
-        <section name="advanced_options" title="Advanced options" expanded="False">
-            <param type="data" name="junction_adapter" argument="-j"
-                   label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa"
-                   multiple="False"/>
-            <param type="text" name="tab_adapter" argument="-M"
-                   label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/>
-            <param type="boolean" name="barcode" argument="-b"
-                   label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False"
-                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="text" name="cut" argument="-c"
-                   label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode"
-                   optional="False" value="0, 0"/>
-            <param type="boolean" name="filter_degenerative_reads" argument="-n"
-                   label="Whether to filter out highly degenerative reads" optional="False" checked="False"
-                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u"
-                   label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False"
-                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False"
-                   multiple="False">
-                <option value="sanger" selected="false">sanger</option>
-                <option value="solexa" selected="false">solexa</option>
-                <option value="auto" selected="true">auto</option>
-            </param>
-            <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format"
-                   optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME"
-                   optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False"
-                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-            <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads"
-                   optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
-        </section>
-    </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} running log" from_work_dir="warnings_and_errors.txt"
-              hidden="false"/>
-        <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 ${on_string}"
-              hidden="false"/>
-        <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}"
-              hidden="false"/>
-    </outputs>
-    <help>
-        <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
-    <citations>
+  <inputs>
+        <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger" multiple="False"/><param type="data" name="second_reads" label="Second reads" help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only." optional="True" format="fastq,fastqsanger" multiple="False"/><param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads." optional="True" format="fasta,fa" multiple="False"/><param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads" optional="True" format="fasta,fa" multiple="False"/><param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False"><option value="None" selected="true">--select a model--</option><option value="head" selected="false">5&#x2019; end trimming (single end reads)</option><option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option><option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option><option value="pe" selected="false">paired-end trimming</option><option value="mp" selected="false">mate-pair trimming</option><option value="ap" selected="false">amplicon trimming</option></param><param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate" optional="False" value="0.1" min="0" max="0.5"/><param type="float" name="maximum_allowed_indel_error_rate" argument="-d" label="Maximum allowed indel error rate" help="The valid range of indel error rate is [0,  maximum allowed error rate]" optional="False" value="0.03" min="0"/><param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming" optional="False" value="0"/><param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality" optional="False" value="0"/><param type="integer" name="minimum_read_length" argument="-l" label="Minimum read length allowed after trimming" optional="False" value="18"/><section name="advanced_options" title="Advanced options" expanded="False"><param type="data" name="junction_adapter" argument="-j" label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa" multiple="False"/><param type="text" name="tab_adapter" argument="-M" label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/><param type="boolean" name="barcode" argument="-b" label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="text" name="cut" argument="-c" label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode" optional="False" value="0, 0"/><param type="boolean" name="filter_degenerative_reads" argument="-n" label="Whether to filter out highly degenerative reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u" label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False" multiple="False"><option value="sanger" selected="false">sanger</option><option value="solexa" selected="false">solexa</option><option value="auto" selected="true">auto</option></param><param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></section></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" from_work_dir="warnings_and_errors.txt" hidden="false"/><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 ${on_string}" hidden="false"/><data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}" hidden="false"/></outputs>
+  <help><![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
+  <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
@@ -130,8 +52,7 @@
             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},
@@ -139,8 +60,7 @@
             year={2015},
             publisher={CRC Press}
             }
-        ]]></citation>
-        <citation type="bibtex"><![CDATA[@article{jiang2014skewer,
+        ]]></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},
@@ -149,6 +69,5 @@
   pages={182},
   year={2014},
   publisher={BioMed Central}
-}]]></citation>
-    </citations>
+}]]></citation></citations>
 </tool>