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

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

<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**

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.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**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

 </help>
</tool>

35:95d75b35e4d2

<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"/>

			<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_, 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.

		.. _Mothur: http://www.mothur.org/wiki/Main_Page

		**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

	</help>
</tool>