Mercurial > repos > lecorguille > camera_annotate

--- a/abims_CAMERA_annotateDiffreport.xml	Mon Apr 25 11:06:25 2016 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Mon Jul 04 08:52:04 2016 -0400
@@ -47,10 +47,8 @@
             mzdec $options.mzdec
             new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #end if
-
-        #if $zip_file:
-            zipfile $zip_file
-        #end if
+
+        @COMMAND_ZIPFILE_LOAD@

     ]]></command>

@@ -126,9 +124,8 @@
             <when value="hide">
             </when>
         </conditional>
-
-        <!-- To pass planemo test -->
-        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
+
+        <expand macro="zipfile_load"/>
     </inputs>

     <outputs>
@@ -210,7 +207,8 @@
             <param name="options|w" value="640"/>
             <param name="options|mzdec" value="2"/>
             <param name="options|sortpval" value="False"/>
-            <param name="zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
+            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
             <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
             <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
         </test>
--- a/macros.xml	Mon Apr 25 11:06:25 2016 -0400
+++ b/macros.xml	Mon Jul 04 08:52:04 2016 -0400
@@ -20,7 +20,27 @@
     <token name="@COMMAND_CAMERA_SCRIPT@">
         LANG=C Rscript $__tool_directory__/CAMERA.r
     </token>
-
+
+    <!-- zipfile load for planemo test -->
+    <token name="@COMMAND_ZIPFILE_LOAD@">
+        #if $zipfile_load_conditional.zip_file:
+        zipfile $zipfile_load_conditional.zip_file
+        #end if
+    </token>
+    <xml name="zipfile_load">
+        <conditional name="zipfile_load_conditional">
+            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
+                <option value="no" >no need</option>
+                <option value="yes" selected="peakgroups">yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+            </when>
+        </conditional>
+    </xml>
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
--- a/planemo_test.sh	Mon Apr 25 11:06:25 2016 -0400
+++ b/planemo_test.sh	Mon Jul 04 08:52:04 2016 -0400
@@ -7,7 +7,7 @@
 # after having installing package on a local galaxy instance
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
-planemo test --install_galaxy --galaxy_branch "dev"
+planemo test --install_galaxy

 #All 1 test(s) executed passed.
 #abims_CAMERA_annotateDiffreport[0]: passed
@@ -16,14 +16,14 @@
 # -- Use of conda dependencies
 planemo conda_init --conda_prefix /tmp/mc
 planemo conda_install --conda_prefix /tmp/mc .
-planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution

 #All 1 test(s) executed passed.
 #abims_CAMERA_annotateDiffreport[0]: passed


 # -- Use of shed_test
-planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch "dev"
+planemo shed_test --install_galaxy -t testtoolshed

 #All 1 test(s) executed passed.
 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: passed