# HG changeset patch
# User greg
# Date 1487688232 18000
# Node ID 7c3ef587aed93e30c822e3ba98111779d64bcec3
# Parent  9eb54f2ef3213a0442416e89b83324bd89cdf9c9
Uploaded

diff -r 9eb54f2ef321 -r 7c3ef587aed9 multigps.xml
--- a/multigps.xml	Fri Feb 17 08:17:12 2017 -0500
+++ b/multigps.xml	Tue Feb 21 09:43:52 2017 -0500
@@ -26,9 +26,6 @@
             #if str($ctrl) != 'None':
                 --ctrl '$ctrl'
             #end if
-            #if str($verbose) == 'yes':
-                --verbose
-            #end if
             --threads=\${GALAXY_SLOTS:-4}
             --geninfo '$chromInfo'
             ############################
@@ -177,10 +174,6 @@
             <validator type="unspecified_build" />
         </param>
         <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
-        <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
-            <option value="no" selected="True">No</option>
-            <option value="yes">Yes</option>
-        </param>
         <!--
         ############################
         ## Advanced options
@@ -407,12 +400,6 @@
             </when>
             <when value="hide" />
         </conditional>
-        <!--
-        <param name="output_process_log" type="select" label="Output MultiGPS process log?">
-            <option value="no" selected="True">No</option>
-            <option value="yes">Yes</option>
-        </param>
-        -->
     </inputs>
     <outputs>
         <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
@@ -421,17 +408,15 @@
     </outputs>
     <tests>
         <test>
-            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
-            <param name="verbose" value="no" />
+            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
             <param name="advanced_options_cond" value="hide" />
             <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
             <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
             <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
         </test>
         <test>
-            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
-            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="sacCer3" />
-            <param name="verbose" value="no" />
+            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="hg19" />
+            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="hg19" />
             <param name="advanced_options_cond" value="display" />
             <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
             <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
@@ -473,7 +458,7 @@
 
 * **Running MultiGPS:**
 
- - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
+ - **Optional binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
  - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
  - **Perform binding model updates?** - Perform binding model updates?
  - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution