# HG changeset patch
# User thanhlv
# Date 1579278554 0
# Node ID 9b1daaba9e8d1c6bb82b307398536ba2e78735eb
# Parent  d0c6d41a0a22f0909e7d79525a6a1df0f2da9d0d
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 44b6f6a2bdcd4ba2dabc3d65c7feefcd2ff3b6db-dirty"

diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_add_tags.xml
--- a/biotradis_add_tags.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_add_tags.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -8,14 +8,14 @@
     
     add_tradis_tags -b $input_bam -o added -v > $log
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
+        <param name="input_bam" type="data" format="bam" label="BAM file"/>
     </inputs>
 
     <outputs>
-       <data name="log" format="txt" label="${tool.name} on ${on_string} Log" />
-       <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string} Log" />
+        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" />
     </outputs>
 
     <tests>
@@ -29,6 +29,6 @@
         Options:
         -b  : bam file with tradis tags
         -v  : verbose debugging output
-    ]]></help>
-
+    ]]>    </help>
+    <expand macro="citations" />
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_bacteria_tradis.xml
--- a/biotradis_bacteria_tradis.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_bacteria_tradis.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -23,46 +23,55 @@
                         -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*
-    ]]></command>
+                    $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="tag" type="text" label="Tag" help="Tag to search for" />
+        <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)" >
+        <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" help="(optional. default = 0)" />
-        <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" />
-        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" />
-        <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" />
+        <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 ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>   
-        <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> 
+        <collection name="insert_plots" format="gz" type="list" label="Insert size plots">
+            <discover_datasets pattern="__name_and_ext__" directory="plots" visible="true" />
+        </collection>
+        <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files">
+            <filter>out_bam is True</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" />
+        </collection>
+        <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
     </outputs>
-  
+
     <help>
-    <![CDATA[
+        <![CDATA[
         Run a TraDIS analysis. This involves:
         1: filtering the data with tags matching that passed via -t option
         2: removing the tags from the sequences
@@ -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)
@@ -88,6 +99,7 @@
         -v        : verbose debugging output
 
         Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_check_tags.xml
--- a/biotradis_check_tags.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_check_tags.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -10,7 +10,7 @@
 
     ]]></command>
     <inputs>
-         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
+         <param name="input_bam" type="data" format="bam" label="BAM file" />
      </inputs>
 
     <outputs>
@@ -29,5 +29,5 @@
         -b  : bam file with tradis tags
         -v  : verbose debugging output
     ]]></help>
-
+    <expand macro="citations" />
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_filter_tags.xml
--- a/biotradis_filter_tags.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_filter_tags.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -8,16 +8,16 @@
     
     filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
-         <param name="tag" type="text" label="Tags to filter" help="" />
-         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
-         <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
+        <param name="tag" type="text" label="Tags to filter" help="" />
+        <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" />
+        <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" />
     </inputs>
 
     <outputs>
-       <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" />
+        <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" />
     </outputs>
 
     <!-- <tests>
@@ -31,6 +31,7 @@
         Options:
         -b  : bam file with tradis tags
         -v  : verbose debugging output
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_plot.xml
--- a/biotradis_plot.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_plot.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -8,14 +8,14 @@
     
     tradis_plot -b $input_bam -m $mapping_quality
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
-         <param name="mapping_quality" type="integer" value="30" label="mapping quality must be greater than X " help="(optional. default: 30)" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="mapping_quality" type="integer" min="0" value="30" label="mapping quality must be greater than X " />
     </inputs>
 
     <outputs>
-       <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" />
+        <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Plot" from_work_dir="tradis.plot" />
     </outputs>
 
     <tests>
@@ -29,6 +29,7 @@
         Options:
         -b  : bam file with tradis tags
         -v  : verbose debugging output
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_remove_tags.xml
--- a/biotradis_remove_tags.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_remove_tags.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -6,18 +6,18 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
     
-    remove_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log
+    remove_tradis_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" />
-         <param name="tag" type="text" label="Tags to remove" help="" />
-         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
+        <param name="input_fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Fastq file"/>
+        <param name="tag" type="text" label="Tags to remove" />
+        <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" />
     </inputs>
 
     <outputs>
-       <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
-       <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
+        <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" />
     </outputs>
 
     <tests>
@@ -31,6 +31,7 @@
         Options:
         -b  : bam file with tradis tags
         -v  : verbose debugging output
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d biotradis_tradis_comparison.xml
--- a/biotradis_tradis_comparison.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/biotradis_tradis_comparison.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -31,10 +31,10 @@
         <conditional name="filter">
             <param name="filter_selector" type="select" label="Filter">
                 <option value="yes">Yes</option>
-                <option value="no" selected="true" >No</option>
+                <option value="no" selected="true">No</option>
             </param>
             <when value="yes">
-                <param name="cutoff" type="integer" value="" label="Cut-off value"/>
+                <param name="cutoff" type="integer" min="0" value="0" label="Cut-off value"/>
             </when>
             <when value="no"/>
         </conditional>
@@ -51,14 +51,10 @@
         </test>
     </tests>
     <help><![CDATA[
-        Adds transposon sequence and quality tags to the read strings and
-        outputs a BAM.
-
-        Usage: add_tags -b file.bam [options]
-
-        Options:
-        -b  : bam file with tradis tags
-        -v  : verbose debugging output
+        Compares two experimental conditions using the method of Dembek et al.
+        mBio 2015. Read counts per gene are compared using edgeR. This analysis
+        requires experimental replicates.
     ]]>    </help>
+    <expand macro="citations" />
 
 </tool>
diff -r d0c6d41a0a22 -r 9b1daaba9e8d macros.xml
--- a/macros.xml	Wed Oct 23 10:38:57 2019 -0400
+++ b/macros.xml	Fri Jan 17 16:29:14 2020 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">1.4.1.dev</token>
+    <token name="@VERSION@">1.4.5</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">biotradis</requirement>