changeset 17:32bb3debd588 draft

Uploaded

--- a/deepTools_macros.xml	Thu Nov 28 13:22:04 2013 -0500
+++ b/deepTools_macros.xml	Fri Dec 06 11:28:08 2013 -0500
@@ -27,10 +27,10 @@
                     label ="Include zeros"
                     help  ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
 
-                <param name="zMin" type="integer" value="" label="Minimum value for the heatmap intensities"
+                <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
                     help="If not specified the value is set automatically."/>
 
-                <param name="zMax" type="integer" value="" label="Maximum value for the heatmap intensities"
+                <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
                     help="If not specified the value is set automatically."/>
 
                 <expand macro="colormap" />
@@ -43,11 +43,12 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement>
+            <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
         </macro>
@@ -104,7 +105,10 @@
             </param>
             <when value="cached">
                 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                    <options from_data_table="deepTools_seqs" />
+                    <options from_data_table="deepTools_seqs">
+                        <filter type="sort_by" column="1" />
+                        <validator type="no_options" message="No indexes are available." />
+                    </options>
                 </param>
             </when>
             <when value="history">

--- a/tool_dependencies.xml	Thu Nov 28 13:22:04 2013 -0500
+++ b/tool_dependencies.xml	Fri Dec 06 11:28:08 2013 -0500
@@ -15,6 +15,9 @@
     <package name="pysam" version="0.7.7">
         <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="bx-python" version="12_2013">
+        <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
 
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
@@ -54,23 +57,25 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">
+    <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
         <install version="1.0">
             <actions>
+                <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
                     <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.7.7" />
                     </repository>
+                    <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="12-2013" />
+                    </repository>
                 </action>
-                <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action>
+                <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                     python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
-
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
@@ -79,6 +84,9 @@
                 </action>
              </actions>
          </install>
-         <readme>Installation of deepTools from Fidel Ramirez.</readme>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
      </package>
 </tool_dependency>