Mercurial > repos > iuc > export2graphlan

changeset 1:b16989c1e3a7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
author iuc
date Wed, 07 Aug 2019 14:49:12 -0400
parents ed1becc01910
children 635c90a27692
files export2graphlan.xml
diffstat 1 files changed, 91 insertions(+), 80 deletions(-) [+]
line wrap: on
line diff
--- a/export2graphlan.xml	Sat Mar 04 11:44:38 2017 -0500
+++ b/export2graphlan.xml	Wed Aug 07 14:49:12 2019 -0400
@@ -1,16 +1,17 @@
-<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
-    <description></description>
+<tool id="export2graphlan" name="Export to GraPhlAn" version="@VERSION@+@GALAXY_VERSION@">
+    <macros>
+        <token name="@VERSION@">0.20</token>
+        <token name="@GALAXY_VERSION@">galaxy0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.19">export2graphlan</requirement>
+        <requirement type="package" version="@VERSION@">export2graphlan</requirement>
     </requirements>
-    <stdio>
-    </stdio>
     <version_command>
 <![CDATA[
-export2graphlan.py -v
+export2graphlan.py -h | grep "ver."
 ]]>
     </version_command>
-    <command>
+    <command detect_errors="exit_code">
 <![CDATA[
         export2graphlan.py
             --lefse_input '$lefse_input'
@@ -19,62 +20,80 @@
             #end if
             -t '$tree'
             -a '$annotation'
-            #if $annotations
-                --annotations '$annotations'
+            #if str($annotations) != ''
+                --annotations $annotations
             #end if
-            #if $external_annotations
-                --external_annotations '$external_annotations'
+            #if str($external_annotations) != ''
+                --external_annotations $external_annotations
             #end if
-            #if $background_levels
-                --background_levels '$background_levels'
+            #if str($background_levels) != ''
+                --background_levels $background_levels
             #end if
-            #if $background_clades
+            #if str($background_clades) != ''
                 --background_clades '$background_clades'
             #end if
-            #if $background_colors
+            #if str($background_colors) != ''
                 --background_colors '$background_colors'
             #end if
-            #if $title
+            #if str($title) != ''
                 --title '$title'
             #end if
-
-            --title_font_size '$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'
-            --min_font_size '$min_font_size'
-            --max_font_size '$max_font_size'
-            --annotation_legend_font_size '$annotation_legend_font_size'
-            --abundance_threshold '$abundance_threshold'
-
-            #if $most_abundant
-                --most_abundant '$most_abundant'
+            #if str($title_font_size) != ''
+                --title_font_size $title_font_size
+            #end if
+            #if str($def_clade_size) != ''    
+                --def_clade_size $def_clade_size
+            #end if
+            #if str($min_clade_size) != ''
+                --min_clade_size $min_clade_size
+            #end if
+            #if str($max_clade_size) != ''
+                --max_clade_size $max_clade_size
             #end if
-            #if $least_biomarkers
-                --least_biomarkers '$least_biomarkers'
+            #if str($def_font_size) != ''
+                --def_font_size $def_font_size
+            #end if
+            #if str($min_font_size) != ''
+                --min_font_size $min_font_size
+            #end if
+            #if str($max_font_size) != ''
+                --max_font_size $max_font_size
+            #end if
+            #if str($annotation_legend_font_size) != ''
+                --annotation_legend_font_size $annotation_legend_font_size
+            #end if
+            #if str($abundance_threshold) != ''
+                --abundance_threshold $abundance_threshold
             #end if
-
-            --fname_row '$fname_row'
-            --sname_row '$sname_row'
-
-            #if $metadata_rows
-                --metadata_rows '$metadata_rows'
+            #if str($most_abundant) != ''
+                --most_abundant $most_abundant
+            #end if
+            #if str($least_biomarkers) != ''
+                --least_biomarkers $least_biomarkers
             #end if
-            #if $skip_rows  
-                --skip_rows '$skip_rows'
+            #if str($title_font_size) != ''
+                --fname_row $fname_row
+            #end if
+            #if str($title_font_size) != ''
+                --sname_row $sname_row
+            #end if
+            #if str($metadata_rows) != ''
+                --metadata_rows $metadata_rows
             #end if
-            #if $sperc
-                --sperc '$sperc'
+            #if str($skip_rows) != ''
+                --skip_rows $skip_rows
             #end if
-            #if $fperc
-                --fperc '$fperc'
+            #if str($sperc) != ''
+                --sperc $sperc
             #end if
-            #if $stop
-                --stop '$stop'
+            #if str($fperc) != ''
+                --fperc $fperc
             #end if
-            #if $ftop
-                --ftop '$ftop'
+            #if str($stop) != ''
+                --stop $stop
+            #end if
+            #if str($ftop) != ''
+                --ftop $ftop
             #end if
 ]]>
     </command>
@@ -90,31 +109,31 @@
             </when>
             <when value="false"/>
         </conditional>
-        <param argument="--annotations" type="text" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form" optional="True"/>
-        <param argument="--external_annotations" type="text" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form" optional="True"/>
-        <param argument="--background_levels" type="text" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form" optional="True"/>
-        <param argument="--background_clades" type="text" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form" optional="True"/>
-        <param argument="--background_colors" type="text" label="List of color to use for the shaded background" 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" optional="True"/>
-        <param argument="--title" type="text" label="Title of the GraPhlAn plot" optional="True"/>
-        <param argument="--title_font_size" type="integer" value="15" label="Title font size"/>
-        <param argument="--def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers"/>
-        <param argument="--min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers"/>
-        <param argument="--max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers"/>
-        <param argument="--def_font_size" type="integer" value="10" label="Default font size"/>
-        <param argument="--min_font_size" type="integer" value="8" label="Minimum font size"/>
-        <param argument="--max_font_size" type="integer" value="12" label="Maximum font size"/>
-        <param argument="--annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend"/>
-        <param argument="--abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated"/>
-        <param argument="--most_abundant" type="integer" label="Number of clades to highlight" optional="True"/>
-        <param argument="--least_biomarkers" type="integer" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers" optional="True"/>
-        <param argument="--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"/>
-        <param argument="--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"/>
-        <param argument="--metadata_rows" type="integer" label="Row number to use as metadata" optional="True"/>
-        <param argument="--skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated" optional="True"/>
-        <param argument="--sperc" type="float" label="Percentile of sample value distribution for sample selection" optional="True"/>
-        <param argument="--fperc" type="float" label="Percentile of feature value distribution for sample selection" optional="True"/>
-        <param argument="--stop" type="integer" label="Number of top samples to select" help="The order is based on percentile specified by --sperc" optional="True"/>
-        <param argument="--ftop" type="integer" label="Number of top features to select" help="The order is based on percentile specified by --fperc" optional="True"/>
+        <param argument="--annotations" type="text" optional="True" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form"/>
+        <param argument="--external_annotations" type="text" optional="True" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form"/>
+        <param argument="--background_levels" type="text" optional="True" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form"/>
+        <param argument="--background_clades" type="text" optional="True" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form"/>
+        <param argument="--background_colors" type="text" optional="True" label="List of color to use for the shaded background" 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"/>
+        <param argument="--title" type="text" optional="True" label="Title of the GraPhlAn plot" />
+        <param argument="--title_font_size" type="integer" optional="True" label="Title font size"/>
+        <param argument="--def_clade_size" type="integer" optional="True" label="Default size for clades that are not found as biomarkers"/>
+        <param argument="--min_clade_size" type="integer" optional="True" label="Minimum value of clades that are biomarkers"/>
+        <param argument="--max_clade_size" type="integer" optional="True" label="Maximum value of clades that are biomarkers"/>
+        <param argument="--def_font_size" type="integer" optional="True" label="Default font size"/>
+        <param argument="--min_font_size" type="integer" optional="True" label="Minimum font size"/>
+        <param argument="--max_font_size" type="integer" optional="True" label="Maximum font size"/>
+        <param argument="--annotation_legend_font_size" type="integer" optional="True" label="Font size for the annotation legend"/>
+        <param argument="--abundance_threshold" type="float" optional="True" label="Minimun abundance value for a clade to be annotated"/>
+        <param argument="--most_abundant" type="integer" optional="True" label="Number of clades to highlight"/>
+        <param argument="--least_biomarkers" type="integer" optional="True" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers"/>
+        <param argument="--fname_row" type="integer" optional="True" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix"/>
+        <param argument="--sname_row" type="integer" optional="True" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix"/>
+        <param argument="--metadata_rows" type="integer" optional="True" label="Row number to use as metadata"/>
+        <param argument="--skip_rows" type="text" optional="True" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated"/>
+        <param argument="--sperc" type="float" optional="True" label="Percentile of sample value distribution for sample selection"/>
+        <param argument="--fperc" type="float" optional="True" label="Percentile of feature value distribution for sample selection"/>
+        <param argument="--stop" type="integer" optional="True" label="Number of top samples to select" help="The order is based on percentile specified by --sperc"/>
+        <param argument="--ftop" type="integer" optional="True" label="Number of top features to select" help="The order is based on percentile specified by --fperc"/>
     </inputs>
     <outputs>
         <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
@@ -139,16 +158,8 @@
             <param name="max_font_size" value="12"/>
             <param name="annotation_legend_font_size" value="10"/>
             <param name="abundance_threshold" value="20.0"/>
-            <param name="most_abundant" value=""/>
-            <param name="least_biomarkers" value=""/>
             <param name="fname_row" value="0"/>
             <param name="sname_row" value="0" />
-            <param name="metadata_rows" value=""/>
-            <param name="skip_rows" value=""/>
-            <param name="sperc" value=""/>
-            <param name="fperc" value=""/>
-            <param name="stop" value=""/>
-            <param name="ftop" value=""/>
             <output name="annotation" file="annotation_output.txt"/>
             <output name="tree" file="tree_output.txt"/>
         </test>