changeset 4:9b67a50799e9 draft

planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791

--- a/proteinortho_macros.xml	Tue Jan 04 18:45:05 2022 +0000
+++ b/proteinortho_macros.xml	Tue Nov 22 16:50:38 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@TOOL_VERSION@">6.0.32</token>
-   <token name="@WRAPPER_VERSION@">0</token>
+   <token name="@TOOL_VERSION@">6.1.2</token>
+   <token name="@WRAPPER_VERSION@">1</token>
    <token name="@PROFILE@">20.09</token>
    <xml name="citations">
         <citations>
@@ -14,10 +14,10 @@
             <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement>
             <!-- blast, blat, and last are not in the biopython requirements
                  diamond is, but latest version does not work: https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/55 -->
-            <requirement type="package" version="2.0.9">diamond</requirement>
-            <requirement type="package" version="2.12.0">blast</requirement>
-            <requirement type="package" version="36">blat</requirement>
-            <requirement type="package" version="1257">last</requirement>
+            <requirement type="package" version="2.0.15">diamond</requirement>
+            <requirement type="package" version="2.13.0">blast</requirement>
+            <requirement type="package" version="377">ucsc-blat</requirement>
+            <requirement type="package" version="1418">last</requirement>
         </requirements>
     </xml>
     <xml name="version_command">

--- a/proteinortho_summary.xml	Tue Jan 04 18:45:05 2022 +0000
+++ b/proteinortho_summary.xml	Tue Nov 22 16:50:38 2022 +0000
@@ -6,27 +6,33 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
+        export TERM=dumb &&
+        ## TODOs:
+        ## - check if 2>&1 can be removed https://gitlab.com/paulklemm_PHD/proteinortho/-/merge_requests/9
+        ## - include output0.tsv as Galaxy output?
         proteinortho_summary.pl 
             $queryfile
             #if $queryfile2:
                 '$queryfile2'
             #end if
-            2>&1 | awk '/^$/ && !f{f=1;next}1' | awk -v RS= '{print > ("output" NR ".tsv")}' 
+            2>&1 
+            | awk '/^$/ && !f{f=1;next}1' ## remove potentially present 1st empty line
+            | awk 'BEGIN{i=0} /^$/{i+=1}{print > ("output" i ".tsv")}' ## split file at empty lines
         &&
-        mv output1.tsv adjacencyMat.tsv &&
-        mv output2.tsv average1paths.tsv &&
-        mv output3.tsv adjacencyMatSquared.tsv &&
-        mv output4.tsv average2paths.tsv
+        mv output1.tsv '$adjacencyMat' &&
+        mv output2.tsv '$average1paths' &&
+        mv output3.tsv '$adjacencyMatSquared' &&
+        mv output4.tsv '$average2paths'
     ]]></command>
     <inputs>
         <param name="queryfile" type="data" format="tabular" label="A orthology-pairs / RBH file"/>
         <param name="queryfile2" type="data" format="tabular" optional="true" label="(optional) A second orthology-pairs / RBH file" help="If you provide a second file, then difference is calculated (GRAPH - second GRAPH)"/>
     </inputs>
     <outputs>
-        <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix" from_work_dir="adjacencyMat.tsv"/>
-        <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges" from_work_dir="average1paths.tsv"/>
-        <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths" from_work_dir="adjacencyMatSquared.tsv"/>
-        <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths" from_work_dir="average2paths.tsv"/>
+        <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix"/>
+        <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges"/>
+        <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths"/>
+        <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths"/>
     </outputs>
     <tests>
         <test expect_num_outputs="4">
@@ -35,24 +41,28 @@
                 <assert_contents>
                     <has_text text="18"/>
                     <has_text text="14"/>
+                    <has_text text="TERM" negate="true"/>
                 </assert_contents>
             </output>
             <output name="average1paths">
                 <assert_contents>
                     <has_text text="9.6"/>
                     <has_text text="15"/>
+                    <has_text text="TERM" negate="true"/>
                 </assert_contents>
             </output>
             <output name="adjacencyMatSquared">
                 <assert_contents>
                     <has_text text="750"/>
                     <has_text text="74"/>
+                    <has_text text="TERM" negate="true"/>
                 </assert_contents>
             </output>
             <output name="average2paths">
                 <assert_contents>
                     <has_text text="1088.8"/>
                     <has_text text="1374.2"/>
+                    <has_text text="TERM" negate="true"/>
                 </assert_contents>
             </output>
         </test>
@@ -63,6 +73,7 @@
                 <assert_contents>
                     <has_text text="49.6"/>
                     <has_text text="59.8"/>
+                    <has_text text="TERM" negate="true"/>
                 </assert_contents>
             </output>
         </test>