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diff mothur/tools/mothur/make.fastq.xml @ 35:95d75b35e4d2

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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents 49058b1f8d3f
children
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--- a/mothur/tools/mothur/make.fastq.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/make.fastq.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,48 +1,65 @@
-<tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0">
- <description>Convert fasta and quality to fastq</description>
- <command interpreter="python">
-  mothur_wrapper.py 
-  --cmd='make.fastq'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq
-  --outputdir='$logfile.extra_files_path'
-  --fasta=$fasta
-  --qfile=$qfile
- </command>
- <inputs>
-  <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
-  <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq">
-   <change_format>
-    <when input="qfile.ext" value="qual454" format="fastqsanger"/>
-    <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
-    <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/>
-    <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
-   </change_format>
-  </data>
- </outputs>
- <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
+<tool id="mothur_make_fastq" name="Make.fastq" version="1.20.0">
+	<description>Convert fasta and quality to fastq</description>
+	<command interpreter="python">
+		mothur_wrapper.py 
+		--cmd='make.fastq'
+		--result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq
+		--outputdir='$logfile.extra_files_path'
+		--fasta=$fasta
+		--qfile=$qfile
+		#if $chooseformat.use: 
+		--format=$chooseformat.format
+		#end if
+	</command>
+	<inputs>
+		<param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
+		<param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
+
+		<conditional name = "chooseformat">
+ 			<param name = "use" type ="boolean" truevalue ="yes" falsevalue="no" label="choose what format your sequences are"/>
 
-Mothur_, initiated by Dr. Patrick Schloss and his software development team 
-in the Department of Microbiology and Immunology at The University of Michigan,  
-provides bioinformatics for the microbial ecology community.
+			<when value = "yes">
+				<param name = "format" type = "select" optional = "true" multiple = "true">
+					<option value = "sanger" selected="true">sanger</option>
+					<option value = "solexa">solexa</option>
+					<option value = "illumina">illumina</option>
+					<option value = "illumina">illumina1.8+</option>
+				</param>
+			</when>
+			<when value = "no"/>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+		<data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq">
+			<change_format>
+				<when input="qfile.ext" value="qual454" format="fastqsanger"/>
+				<when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
+				<when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/>
+				<when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
+			</change_format>
+		</data>
+	</outputs>
+	<requirements>
+		<requirement type="package" version="1.33">mothur</requirement>
+	</requirements>
+	<tests>
+	</tests>
+	<help>
+		**Mothur Overview**
 
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
+		Mothur_, initiated by Dr. Patrick Schloss and his software development team 
+		in the Department of Microbiology and Immunology at The University of Michigan,  
+		provides bioinformatics for the microbial ecology community.
 
-**Command Documenation**
+		.. _Mothur: http://www.mothur.org/wiki/Main_Page
 
-The fastq.info_ command reads a fasta file and quality file and creates a fastq.
+		**Command Documenation**
+
+		The fastq.info_ command reads a fasta file and quality file and creates a fastq.
 
 
-.. _fastq.info: http://www.mothur.org/wiki/Make.fastq
+		.. _fastq.info: http://www.mothur.org/wiki/Make.fastq
 
- </help>
+	</help>
 </tool>