# HG changeset patch
# User thanhlv
# Date 1579278756 18000
# Node ID cbe965d49727a9becca9230c17a3b28b37167224
# Parent  99427def7645a68dcf5fce82d5c2892c4965ab61
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 44b6f6a2bdcd4ba2dabc3d65c7feefcd2ff3b6db-dirty"

diff -r 99427def7645 -r cbe965d49727 biotradis_bacteria_tradis.xml
--- a/biotradis_bacteria_tradis.xml	Fri Dec 06 10:15:14 2019 -0500
+++ b/biotradis_bacteria_tradis.xml	Fri Jan 17 11:32:36 2020 -0500
@@ -23,41 +23,50 @@
                         -td $tag_dir
                         -mm $mm
                         -m $m
-                    #if str($smalt_k)!=""
+                    #if $smalt:
+                        $smalt
+                        #if str($smalt_k)!=""
                         --smalt_k $smalt_k
-                    #end if
-                    #if str($smalt_s)!=""
-                        --smalt_s $smalt_s
-                    #end if
+                        #end if
+                        #if str($smalt_s)!=""
+                            --smalt_s $smalt_s
+                        #end if
                         --smalt_y $smalt_y
                         --smalt_r $smalt_r
                         -n "\${GALAXY_SLOTS:-2}"
-                    #if $verbose
-                        --verbose
                     #end if
-                    && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
-                    && tar cvzf mapped.tar.gz *mapped.bam*
+                    $verbose
+                    && mkdir plots bams
+                    && mv *insert_site_plot.gz ./plots
+                    && mv *mapped.bam* ./bams
     ]]>    </command>
     <inputs>
-        <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" />
+        <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" help="Support multiple files"/>
         <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" />
         <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
         <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)">
             <option value="3" selected="true">3</option>
             <option value="5">5</option>
         </param>
-        <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" />
-        <param name="m" type="integer" value="30" label="Mapping quality cutoff score" />
-        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" />
-        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" />
-        <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" />
-        <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT" />
+        <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag"/>
+        <param name="m" type="integer" value="30" label="Mapping quality cutoff score"/>
+        <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/>
+        <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" />
+        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/>
+        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/>
+        <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/>
+        <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/>
         <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
     </inputs>
 
     <outputs>
-        <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/>
-        <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>
+        <collection name="insert_plots" format="gz" type="list" label="Insert size plots">
+            <discover_datasets pattern="__name_and_ext__" directory="plots" visible="true" />
+        </collection>
+        <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files">
+            <filter>out_bam is True</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" />
+        </collection>
         <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
     </outputs>
 
@@ -74,11 +83,13 @@
 
         Options:
         -f        : text file listing fastq files with tradis tags attached
-        -t        : tag to search for
+        -t        : tag to search for (optional.  If not set runs bwa in tagless mode with no filtering.)
         -r        : reference genome in fasta format (.fa)
         -td       : tag direction - 3 or 5 (optional. default = 3)
         -mm       : number of mismatches allowed when matching tag (optional. default = 0)
         -m        : mapping quality cutoff score (optional. default = 30)
+        -k        : custom k-mer value (min seed length) (optional)
+        --smalt   : use smalt rather than bwa as the mapper
         --smalt_k : custom k-mer value for SMALT mapping (optional)
         --smalt_s : custom step size for SMALT mapping (optional)
         --smalt_y : custom y parameter for SMALT (optional. default = 0.96)