diff make.fastq.xml @ 0:c49147967884 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.fastq.xml	Fri May 19 05:33:34 2017 -0400
@@ -0,0 +1,88 @@
+<tool profile="16.07" id="mothur_make_fastq" name="Make.fastq" version="@WRAPPER_VERSION@.0">
+    <description>Convert fasta and quality to fastq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$qfile" qfile.dat &&
+
+        echo 'make.fastq(
+            fasta=fasta.dat,
+            qfile=qfile.dat
+            #if $chooseformat.use == "yes":
+                ,format=${chooseformat.format}
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
+        <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
+        <conditional name="chooseformat">
+            <param name="use" type="select" label="Choose quality format for your output sequences are" help="If none selected, this tool will keep the format of input qfile">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="format" type="select" optional="true" multiple="true">
+                    <option value="sanger" selected="true">sanger</option>
+                    <option value="illumina1.8+">Illumina 1.8+</option>
+                    <option value="illumina">Illumina</option>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq">
+            <change_format><!-- if set, chooseformat.format param should override qfile.ext format -->
+                <when input="qfile.ext" value="qual454" format="fastqsanger"/>
+                <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
+                <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
+                <when input="chooseformat.format" value="sanger" format="fastqsanger"/>
+                <when input="chooseformat.format" value="illumina1.8+" format="fastqsanger"/>
+                <when input="chooseformat.format" value="illumina" format="fastqillumina"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test defaults -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
+            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
+            <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with quality score format conversion -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
+            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
+            <param name="use" value="yes"/>
+            <param name="format" value="illumina"/>
+            <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The fastq.info_ command reads a fasta file and quality file and creates a fastq.
+
+
+.. _fastq.info: https://www.mothur.org/wiki/Make.fastq
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>