Mercurial > repos > bebatut > export2graphlan

changeset 1:f7e87cc38f57 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
author bebatut
date Thu, 31 Mar 2016 03:58:09 -0400
parents f3a11239c704
children d2b9ea71c6ed
files export2graphlan.xml
diffstat 1 files changed, 33 insertions(+), 84 deletions(-) [+]
line wrap: on
line diff
--- a/export2graphlan.xml	Mon Feb 01 07:45:45 2016 -0500
+++ b/export2graphlan.xml	Thu Mar 31 03:58:09 2016 -0400
@@ -14,13 +14,13 @@
 
     <version_command>
 <![CDATA[
-python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py -v
+python export2graphlan.py -v
 ]]>
     </version_command>
 
     <command>
 <![CDATA[        
-        python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py
+        python export2graphlan.py
             -i $lefse_input
 
             #if $lefse_output
@@ -102,117 +102,66 @@
     </command>
 
     <inputs>
-        <param name="lefse_input" type="data" format="tabular" label="Input file" 
-            help="Identical to LEfSe input file (--lefse_input)"/>
+        <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"/>
+        <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
 
-        <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"/>
+        <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"/>
 
-        <param name="external_annotations" type="text" label="List which levels 
-            should use the external legend for the annotation (Optional)" 
-            help="The levels must be in comma-separated form (--external_annotations)" 
-            optional="True"/>
+        <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/>
 
-        <param name="background_levels" type="text" label="List which levels should 
-            be highlight with a shaded background (Optional)" 
-            help="The levels must be in comma-separated form (--background_levels)" 
-            optional="True"/>
+        <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/>
 
-        <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_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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="fperc" type="float" label="Percentile of feature value 
-            distribution for sample selection (Optional)" help="(--fperc)" 
-            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="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"/>
+        <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>
 
     <outputs>
-        <data format="txt" name="tree" 
-            label="${tool.name} on ${on_string}: Tree" />
-        <data format="txt" name="annotation" 
-            label="${tool.name} on ${on_string}: Annotation" />
+        <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
+        <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
         
     </outputs>