diff chimera.pintail.xml @ 2:a037860aad0b draft

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

--- a/chimera.pintail.xml	Tue Sep 05 16:54:46 2017 -0400
+++ b/chimera.pintail.xml	Tue Mar 20 22:15:06 2018 -0400
@@ -7,83 +7,90 @@
     <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 &&
-        ln -s "$conservation" conservation.dat &&
-        ln -s "$quantile" quantile.dat &&
-        #if $mask.source2 == "history":
-            ln -s "$mask.input" mask.input.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$alignment.reference' alignment.reference.dat &&
+ln -s '$conservation' conservation.dat &&
+ln -s '$quantile' quantile.dat &&
+#if $mask_cond.source2 == "history":
+    ln -s '$mask_cond.mask' mask.dat &&
+#end if
 
-        echo 'chimera.pintail(
-            fasta=fasta.dat,
-            reference=alignment.template.dat,
-            filter=$filter,
-            #if $mask.source2 == "default":
-                mask=default,
-            #elif $mask.source2 == "history":
-                mask=mask.input.dat,
-            #end if
-            #if $conservation:
-                conservation=conservation.dat,
-            #end if
-            #if $quantile:
-                quantile=quantile.dat,
-            #end if
-            #if int($window) > 0:
-                window=$window,
-            #end if
-            #if int($increment) > 0:
-                increment=$increment,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chimera.pintail(
+    fasta=fasta.dat,
+    reference=alignment.reference.dat,
+    filter=$filter,
+    #if $mask_cond.source2 == "default":
+        mask=default,
+    #elif $mask_cond.source2 == "history":
+        mask=mask.dat,
+    #end if
+    #if $conservation:
+        conservation=conservation.dat,
+    #end if
+    #if $quantile:
+        quantile=quantile.dat,
+    #end if
+    #if int($window) > 0:
+        window=$window,
+    #end if
+    #if int($increment) > 0:
+        increment=$increment,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
+        <param argument="fasta" type="data" format="fasta" label="fasta - Candiate 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" label="reference - Select an alignment database" help="">
+                <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" label="reference - Reference to align with" help=""/>
+                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
             </when>
         </conditional>
-        <param name="filter" type="boolean" falsevalue="false" truevalue="true" checked="false" label="filter - Apply a 50% soft vertical filter"/>
-        <conditional name="mask">
+        <param argument="filter" type="boolean" falsevalue="false" truevalue="true" checked="false" label="filter - Apply a 50% soft vertical filter"/>
+        <conditional name="mask_cond">
             <param name="source2" type="select" label="Mask option">
                 <option value="">None</option>
                 <option value="default">default ecoli mask</option>
                 <option value="history">From your history</option>
             </param>
             <when value="history">
-                <param name="input" type="data" format="mothur.filter" label="Mask for the template file" help=""/>
+                <param argument="mask" type="data" format="mothur.filter" label="Mask for the template file"/>
             </when>
             <when value=""/>
             <when value="default"/>
         </conditional>
-        <param name="conservation" type="data" format="mothur.freq" optional="true" label="conservation - Template Conserved frequencies" help="a file containing the frequency information for your template file to increase speed. Mothur will generate this for you but it takes a long time."/>
-        <param name="quantile" type="data" format="mothur.quan" optional="true" label="quantile - Template quantile information" help=" file containing the quantiles information for your template file to increase speed. Mothur can generate this for you but it takes a VERY long time. Note that when you use the filter, mask or mask and filter you need to select the appropriate quantile file. The filter parameter makes the quantile file generated specific to the query set you are analyzing."/>
-        <param name="window" type="integer" value="300" label="window - Length of sequence you want in each window analyzed (uses default if &lt; 1)" help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/>
-        <param name="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)" help="Default is 25. Note, changing the increment will require new quantile files to be made."/>
+        <param argument="conservation" type="data" format="mothur.freq" optional="true" label="conservation - Template Conserved frequencies"
+            help="a file containing the frequency information for your template file to increase speed. Mothur will generate this for you but it takes a long time."/>
+        <param argument="quantile" type="data" format="mothur.quan" optional="true" label="quantile - Template quantile information"
+            help=" file containing the quantiles information for your template file to increase speed. Mothur can generate this for you but it takes a VERY long time.
+            Note that when you use the filter, mask or mask and filter you need to select the appropriate quantile file. The filter parameter makes the quantile file
+            generated specific to the query set you are analyzing."/>
+        <param argument="window" type="integer" value="300" label="window - Length of sequence you want in each window analyzed (uses default if &lt; 1)"
+            help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/>
+        <param argument="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)"
+            help="Default is 25. Note, changing the increment will require new quantile files to be made."/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="txt" from_work_dir="fasta.*pintail.chimeras" label="${tool.name} on ${on_string}: pintail.chimeras"/>
+        <data name="pintail.chimeras" format="txt" from_work_dir="fasta.*pintail.chimeras" label="${tool.name} on ${on_string}: pintail.chimeras"/>
         <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*pintail.accnos" label="${tool.name} on ${on_string}: pintail.accnos"/>
-        <data name="out_freq" format="mothur.freq" from_work_dir="alignment.template.freq" label="${tool.name} on ${on_string}: pintail.freq">
+        <data name="out_freq" format="mothur.freq" from_work_dir="alignment.reference.freq" label="${tool.name} on ${on_string}: pintail.freq">
             <filter>conservation == None</filter>
         </data>
         <data name="out_quantile" format="mothur.quan" from_work_dir="*.quan" label="${tool.name} on ${on_string}: pintail.quan">
@@ -94,32 +101,33 @@
         <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="reference" value="HMP_MOCK.v35.align"/>
             <param name="quantile" value="HMP_MOCK.v35.pintail.quan"/>
             <param name="window" value="200"/>
-            <output name="out_file" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/>
+            <output name="pintail.chimeras" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/>
             <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos" ftype="mothur.accnos"/>
+            <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="reference" value="HMP_MOCK.v35.align"/>
             <param name="source2" value="default"/>
             <param name="window" value="200"/>
-            <output name="out_file" ftype="txt">
+            <output name="pintail.chimeras" ftype="txt">
                 <assert_contents>
                     <has_text text="Observed"/>
                     <has_text text="Expected"/>
                 </assert_contents>
             </output>
-            <output name="out_quantile" md5="23a665c9bace6b73efaae1ecf6d88c59" ftype="mothur.quan"/>
-            <output name="out_freq" md5="0381c5adade485cc4341a0ef5674f4d8" ftype="mothur.freq"/>
+            <output name="out_quantile" md5="74372024214704010aed4f9c8258f77b" ftype="mothur.quan"/>
+            <output name="out_freq" md5="2d2c4066c5de06c8d1d78ee3784daa3d" ftype="mothur.freq"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -143,8 +151,7 @@
 .. _paper: http://www.ncbi.nlm.nih.gov/pubmed/16332745
 .. _chimera.pintail: https://www.mothur.org/wiki/Chimera.pintail
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1128/AEM.71.12.7724-7736.2005</citation>
     </expand>