diff raceid_filtnormconf.xml @ 4:5d5b14dbd092 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"

--- a/raceid_filtnormconf.xml	Mon Apr 15 17:55:17 2019 -0400
+++ b/raceid_filtnormconf.xml	Mon Aug 12 12:59:06 2019 -0400
@@ -1,27 +1,11 @@
-<tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.3" >
-    <description>generates a normalised and filtered count matrix of single-cell RNA data</description>
+<tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
+    <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description>
     <macros>
         <import>macros.xml</import>
-        <import>macros_cluster.xml</import>
+        <import>macros_cheetah.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command><![CDATA[
-Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
-]]>
-    </version_command>
-
-    <command detect_errors="exit_code"><![CDATA[
-#set bin = 'cluster.R'
-Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null
-    ]]></command>
-    <configfiles>
-        <configfile name="userconf" ><![CDATA[
-@STRING2VECTOR@
-
-@FILTNORM_CHEETAH@
-]]>
-        </configfile>
-    </configfiles>
+    <expand macro="version_command_config" prog="cluster.R" cheetah="FILTNORM_CHEETAH" out="2&#62; '$outlog' &#62; /dev/null" />
     <inputs>
         <param name="intable" type="data" format="tabular" label="Count Matrix" />
         <section name="filt" title="Filtering" expanded="true" >
@@ -70,18 +54,26 @@
         </section>
     </inputs>
     <outputs>
+        <data name="outtable" format="tabular" label="${tool.name} on ${on_string}: Normalised Matrix" />
         <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
         <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
         <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics"  />
     </outputs>
     <tests>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
             <param name="intable" value="use.intestinal" />
             <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
             <output name="outlog" value="intestinal.filter.log" />
+            <output name="outtable" >
+                <assert_contents>
+                    <has_n_columns n="288" />
+                    <has_text_matching expression="Amdhd2\s0\.000" />
+                    <has_text_matching expression="Ammecr1(\s0\s0)+" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <!-- defaults, feeding in a matrix with reduced filtering -->
             <param name="intable" value="matrix.tabular" />
             <section name="filt" >
@@ -92,7 +84,7 @@
             <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" />
             <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
             <param name="intable" value="use.intestinal" />
             <section name="filt" >
@@ -107,7 +99,7 @@
             </section>
             <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <!-- defaults, but histogram adjustment  -->
             <param name="intable" value="use.intestinal" />
             <section name="filt" >
@@ -115,7 +107,7 @@
             </section>
             <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <!-- Advanced. Opts, CC used  -->
             <param name="intable" value="use.intestinal" />
             <section name="filt" >