diff make_prefs_file.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_prefs_file.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,47 @@
+<tool id="make_prefs_file" name="make_prefs_file" version="1.2.1">
+ <description>Generate preferences file</description>
+ <requirements>
+  <requirement type="binary">make_prefs_file.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  make_prefs_file.py
+  --map_fname=$map_fname
+  --output_fp=$output_fp
+  --mapping_headers_to_use=$mapping_headers_to_use
+  --background_color=$background_color
+  --monte_carlo_dists=$monte_carlo_dists
+  --input_taxa_file=$input_taxa_file
+  --ball_scale=$ball_scale
+  --arrow_line_color=$arrow_line_color
+  --arrow_head_color=$arrow_head_color
+ </command>
+ <inputs>
+  <param name="map_fname" type="data" format="tabular" label="map_fname"
+   help="This is the metadata mapping file [default=('NO', 'DEFAULT')] [REQUIRED]"/>
+  <param name="mapping_headers_to_use" type="data" format="tabular" label="mapping_headers_to_use"
+   help="mapping fields touse in prefs file [default: ALL]"/>
+  <param name="background_color" type="text" value="black" label="background_color"
+   help="This is the backgroundcolor to  use in the plots. [default: black]"/>
+  <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists"
+   help="monte carlo distanceto use for each sample header [default: 10]"/>
+  <param name="input_taxa_file" type="data" format="txt" label="input_taxa_file"
+   help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/>
+  <param name="ball_scale" type="float" value="1.0" label="ball_scale"
+   help="scale factor for the size of each ball in the plots [default: 1.0]"/>
+  <param name="arrow_line_color" type="text" value="white" label="arrow_line_color"
+   help="arrow line color forprocrustes analysis. [default: white]"/>
+  <param name="arrow_head_color" type="text" value="red" label="arrow_head_color"
+   help="arrow head color forprocrustes analysis. [default: red]"/>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+