diff check_id_map.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_id_map.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,43 @@
+<tool id="check_id_map" name="check_id_map" version="1.2.0">
+ <description>Checks user's metadata mapping file for required data, valid format</description>
+ <requirements>
+  <requirement type="binary">check_id_map.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_outputdir='$log.extra_files_path'
+  --galaxy_datasets='^\S+_corrected\.txt$:'$corrected_mapping,'^\S+\.log:'$log
+  check_id_map.py
+  --map=$map
+  --output_dir='$log.extra_files_path'
+  --char_replace=$char_replace
+  $not_barcoded
+  $variable_len_barcodes
+  $disable_primer_check
+  $verbose
+ </command>
+ <inputs>
+  <param name="map" type="data" format="tabular" label="map"
+   help="Metadata mapping file filepath [REQUIRED]"/>
+  <param name="char_replace" type="text" value="_" label="char_replace"
+   help="Changes the default character used to replace invalid characters found in the mapping file.  Must be a valid character (alphanumeric or underscore).  NOT IMPLEMENTED CURRENTLY [default: _]"/>
+  <param name="not_barcoded" type="boolean" truevalue="--not_barcoded" falsevalue="" checked="false" label="not_barcoded"
+   help="Use -b if barcodes are not present. [default: False]"/>
+  <param name="variable_len_barcodes" type="boolean" truevalue="--variable_len_barcodes" falsevalue="" checked="false" label="variable_len_barcodes"
+   help="Use -B if variable length barcodes are present to suppress warnings about barcodes of unequal length. [default: False]"/>
+  <param name="disable_primer_check" type="boolean" truevalue="--disable_primer_check" falsevalue="" checked="false" label="disable_primer_check"
+   help="Use -p to disable checks for primers. [default: False]"/>
+  <param name="verbose" type="boolean" truevalue="" falsevalue="--verbose" checked="false" label="verbose"
+   help="Turn on this flag to disable verbose output.  [default: True]"/>
+ </inputs>
+ <outputs>
+   <data format="txt" name="log"/>
+   <data format="tabular" name="corrected_mapping" label="${tool.name} on ${on_string}: corrected_mapping"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+