diff chimera.check.xml @ 2:37bd32018025 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/chimera.check.xml	Tue Sep 05 17:15:20 2017 -0400
+++ b/chimera.check.xml	Tue Mar 20 22:20:22 2018 -0400
@@ -7,63 +7,65 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$alignment.template" alignment.template.dat &&
-        #if $svg.gen == "yes":
-            ln -s "$svg.name" svg.name.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$alignment.reference' alignment.reference.dat &&
+#if $svg_cond.svg == "yes":
+    ln -s '$svg_cond.name' svg.name.dat &&
+#end if
 
-        echo 'chimera.check(
-            fasta=fasta.dat,
-            reference=alignment.template.dat,
-            #if $svg.gen == "yes":
-                svg=yes,
-                name=svg.name.dat,
-            #end if
-            increment=$increment,
-            ksize=$ksize,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chimera.check(
+    fasta=fasta.dat,
+    reference=alignment.reference.dat,
+    #if $svg_cond.svg == "yes":
+        svg=yes,
+        name=svg.name.dat,
+    #end if
+    increment=$increment,
+    ksize=$ksize,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/>
+        <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
         <conditional name="alignment">
-            <param name="source" type="select" label="Select Reference Template from" help="">
+            <param name="source" type="select" label="Select Reference Template from">
                 <option value="hist">History</option>
                 <option value="ref">Cached Reference</option>
             </param>
             <when value="ref">
-                <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help="">
-                    <options from_data_table="mothur_aligndb">
-                    </options>
+                <param argument="reference" type="select" label="reference - Select an alignment database">
+                    <options from_data_table="mothur_aligndb"/>
                 </param>
             </when>
             <when value="hist">
-                <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/>
+                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
             </when>
         </conditional>
-        <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
-        <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/>
-        <conditional name="svg">
-            <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
+        <param argument="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments"
+            help="uses default if &lt; 1"/>
+        <param argument="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration"
+            help="Default is 10, but you may set it up to sequence length minus twice the window."/>
+        <conditional name="svg_cond">
+            <param argument="svg" type="select" label="svg - Generate a SVG plot for each query sequence">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/>
+                <param argument="name" type="data" format="mothur.names" optional="true" label="name - Names of queries for which to generate SVG plot"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/>
+        <data name="chimeracheck.chimeras" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/>
         <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\.chimeracheck\.svg"/>
             <filter>svg['gen'] == 'yes'</filter>
@@ -73,26 +75,27 @@
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <param name="source" value="hist"/>
-            <param name="template" value="HMP_MOCK.v35.align"/>
-            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
+            <param name="reference" value="HMP_MOCK.v35.align"/>
+            <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
             <param name="source" value="hist"/>
-            <param name="template" value="HMP_MOCK.v35.align"/>
-            <param name="gen" value="yes"/>
+            <param name="reference" value="HMP_MOCK.v35.align"/>
+            <param name="svg" value="yes"/>
             <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/>
-            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
+            <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
             <output_collection name="images" count="2">
                 <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/>
                 <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -104,7 +107,6 @@
 
 .. _chimera.check: https://www.mothur.org/wiki/Chimera.check
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>