# HG changeset patch
# User bebatut
# Date 1466510701 14400
# Node ID d7cf3b50a0744c958a3cc3971bf0f1a67276887e
# Parent  b344522045f3efa11e94f35a14b3be0e502f9feb
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 3472a70f35769aaeafa40e8fbce97aac2c4ea4f8-dirty

diff -r b344522045f3 -r d7cf3b50a074 export2graphlan.xml
--- a/export2graphlan.xml	Wed Apr 20 06:09:29 2016 -0400
+++ b/export2graphlan.xml	Tue Jun 21 08:05:01 2016 -0400
@@ -19,12 +19,12 @@
     </version_command>
 
     <command>
-<![CDATA[        
+<![CDATA[
         export2graphlan.py
             -i $lefse_input
 
-            #if $lefse_output
-                -o lefse_output
+            #if $input_lefse_output.input_lefse_output_test == "true"
+                -o $input_lefse_output.lefse_output
             #end if
 
             -t $tree
@@ -49,13 +49,13 @@
             #if $background_colors
                 --background_colors "$background_colors"
             #end if
- 
+
             #if $title
                 --title "title"
             #end if
-  
-            --title_font_size $title_font_size 
-            --def_clade_size $def_clade_size 
+
+            --title_font_size $title_font_size
+            --def_clade_size $def_clade_size
             --min_clade_size $min_clade_size
             --max_clade_size $max_clade_size
             --def_font_size $def_font_size
@@ -78,8 +78,8 @@
             #if $metadata_rows
                 --metadata_rows $metadata_rows
             #end if
-                  
-            #if $skip_rows  
+
+            #if $skip_rows
                 --skip_rows $skip_rows
             #end if
 
@@ -104,7 +104,17 @@
     <inputs>
         <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
 
-        <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
+        <conditional name="input_lefse_output">
+            <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help="">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+
+            <when value="true">
+                <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file" help="(--lefse_output)"/>
+            </when>
+            <when value="false"/>
+        </conditional>
 
         <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/>
 
@@ -115,47 +125,28 @@
         <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/>
 
         <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/>
-        
+
         <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
-
         <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
-
         <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/>
-
         <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
-
         <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
-
         <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
-
         <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
-
         <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
-
         <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
-
         <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
-
         <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
 
         <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/>
 
         <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/>
-
         <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/>
-
         <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
-
         <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/>
-
-        <param name="sperc" type="float" label="Percentile of sample value 
-            distribution for sample selection (Optional)" help="(--sperc)" 
-            optional="True"/>
-
+        <param name="sperc" type="float" label="Percentile of sample value distribution for sample selection (Optional)" help="(--sperc)" optional="True"/>
         <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
-
         <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/>
-
         <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/>
     </inputs>
 
@@ -167,6 +158,7 @@
     <tests>
         <test>
             <param name="lefse_input" value="input_profile.tabular"/>
+            <param name="input_lefse_output_test" value="no" />
             <param name="annotations" value=""/>
             <param name="external_annotations" value=""/>
             <param name="background_levels" value=""/>
@@ -198,18 +190,15 @@
     </tests>
 
     <help><![CDATA[
-
 **What it does**
 
-export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
-
-In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 
+export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
 
-For more information, check the 
-`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
+In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
 
+For more information, check the `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
     ]]></help>
 
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r b344522045f3 -r d7cf3b50a074 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 20 06:09:29 2016 -0400
+++ b/tool_dependencies.xml	Tue Jun 21 08:05:01 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="pandas" version="0.16">
-        <repository changeset_revision="ea929a7f2976" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2511234c20da" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.16">
         <repository changeset_revision="80f8536c6dc2" name="package_python_2_7_scipy_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />