diff kc-align.xml @ 8:1c65ddbaeefa draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 000db9fd34a1056bbdd95b007acb5919873fa2b6"

--- a/kc-align.xml	Thu May 14 11:44:15 2020 -0400
+++ b/kc-align.xml	Mon Oct 05 20:09:54 2020 +0000
@@ -1,23 +1,28 @@
-<tool id="kc-align" name="Kc-Align" version="0.2" python_template_version="3.5">
+<tool id="kc-align" name="Kc-Align" version="1.0" python_template_version="3.5">
     <requirements>
-        <requirement type="package" version="0.6.1">kcalign</requirement>
+        <requirement type="package" version="1.0.2">kcalign</requirement>
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
         kc-align
-            --mode $position.mode
-            --reference '$reference'
-            --reads '$reads'
+            --mode '$position.mode'
+            --reference '$ref'
+            --sequences '$seqs'
             #if $position.mode == "genome":
-                --start $position.start
-                --end $position.end
+                --start '$position.start'
+                --end '$position.end'
+                -d '$position.dist'
+            #end if
+            #if $position.mode == "mixed":
+                -d '$position.dist'
             #end if
             $compress
-            --parallel
+            -th '$threads'
+
     ]]></command>
     <inputs>
-        <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
-        <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
+        <param name="ref" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
+        <param name="seqs" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
         <conditional name="position" >
             <param name="mode" type="select" label="Mode" >
                 <option value="genome">Genome</option>
@@ -27,13 +32,26 @@
             <when value="genome" >
                 <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
                 <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
+                <param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
+                    <option value="none">None</option>
+                    <option value="very-close">Very Close</option>
+                    <option value="semi-close">Semi-Close</option>
+                    <option value="less-close">Less Close</option>
+                </param>
             </when>
             <when value="gene" >
             </when>
             <when value="mixed" >
+            	<param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
+                    <option value="none">None</option>
+                    <option value="very-close">Very Close</option>
+                    <option value="semi-close">Semi Close</option>
+                    <option value="less-close">Less Close</option>
+                </param>
             </when>
         </conditional>
         <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
+        <param name="threads" type="integer" argument="-th" value="1" label="Cores" />
     </inputs>
     <outputs>
         <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
@@ -41,13 +59,14 @@
     </outputs>
 <tests>
     <test>
-        <param name="reference" ftype="fasta" value="wuhan_ref.fasta" />
-        <param name="reads" ftype="fasta" value="3.fasta" />
+        <param name="ref" ftype="fasta" value="wuhan_ref.fasta" />
+        <param name="seqs" ftype="fasta" value="3.fasta" />
         <param name="mode" value="genome" />
         <param name="start" value="21563" />
         <param name="end" value="25384" />
-        <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" />
-        <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" />
+        <param name="threads" value="15" />
+        <output name="fasta" ftype="fasta" compare="contains" value="kc-align.fasta" />
+        <output name="clustal" ftype="txt" compare="contains" value="kc-align.clustal" />
     </test>
 </tests>
     <help><![CDATA[