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changeset 1:26abc7846e6f draft

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"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
author iuc
date Tue, 14 Sep 2021 11:39:10 +0000
parents 4850f0d15f01
children a8addd4fb60a
files proteinortho.xml proteinortho_macros.xml
diffstat 2 files changed, 67 insertions(+), 125 deletions(-) [+]
line wrap: on
line diff
--- a/proteinortho.xml	Tue Feb 18 17:57:28 2020 -0500
+++ b/proteinortho.xml	Tue Sep 14 11:39:10 2021 +0000
@@ -1,7 +1,32 @@
-<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
+<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>detects orthologous proteins/genes within different species</description>
     <macros>
         <import>proteinortho_macros.xml</import>
+        <xml name="test_outputs">
+            <output name="proteinortho">
+                <assert_contents>
+                    <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
+                    <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
+                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
+                </assert_contents>
+            </output>
+            <output name="blastgraph">
+                <assert_contents>
+                    <has_line_matching expression="# file_a\tfile_b"/>
+                    <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
+                    <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
+                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
+                </assert_contents>
+            </output>
+            <output name="proteinorthograph">
+                <assert_contents>
+                    <has_line_matching expression="# file_a\tfile_b"/>
+                    <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/>
+                    <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
+                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
+                </assert_contents>
+            </output>
+        </xml>
     </macros>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
@@ -111,23 +136,10 @@
     <tests>
         <test expect_num_outputs="3"> <!-- test normal -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="2&#009;5&#009;0.16"/>
-                    <has_text text="M_640,M_642,M_649"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="L_10&#009;E_10&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="L_11&#009;E_11&#009;"/>
-                </assert_contents>
-            </output>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=diamond"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- various parameter -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
@@ -138,124 +150,51 @@
             <param name="identity" value="42"/>
             <param name="selfblast" value="true"/>
             <param name="singles" value="true"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="1&#009;1&#009;0"/>
-                    <has_text text="&#009;C_177&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="C_1&#009;C_1&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="C_12&#009;C_21&#009;"/>
-                </assert_contents>
-            </output>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=diamond"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- synteny -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
             <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/>
             <param name="synteny_options" value="specified"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="4&#009;5&#009;0.144"/>
-                    <has_text text="E_313,E_315"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="M_313&#009;L_313&#009;"/>
-                </assert_contents>
-            </output>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=diamond"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- blast -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
-            <param name="--p" value="blastp"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="2&#009;5&#009;0.16"/>
-                    <has_text text="M_640,M_642,M_649"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="M_3&#009;L_3&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="M_317&#009;L_317&#009;"/>
-                </assert_contents>
-            </output>
+            <param name="p" value="blastp"/>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=blastp"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- auto blast -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
-            <param name="--p" value="autoblast"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="2&#009;5&#009;0.16"/>
-                    <has_text text="M_640,M_642,M_649"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="M_3&#009;L_3&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="M_317&#009;L_317&#009;"/>
-                </assert_contents>
-            </output>
+            <param name="p" value="autoblast"/>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=autoblast"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- last -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
-            <param name="--p" value="lastp"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="2&#009;5&#009;0.16"/>
-                    <has_text text="M_640,M_642,M_649"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="M_636&#009;E_317&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="E_11&#009;C_11&#009;"/>
-                </assert_contents>
-            </output>
+            <param name="p" value="lastp"/>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=lastp"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="3"> <!-- blat -->
             <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
-            <param name="--p" value="blastp"/>
-            <output name="proteinortho">
-                <assert_contents>
-                    <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
-                    <has_text text="2&#009;5&#009;0.16"/>
-                    <has_text text="M_640,M_642,M_649"/>
-                </assert_contents>
-            </output>
-            <output name="blastgraph">
-                <assert_contents>
-                    <has_text text="E_10&#009;C_10&#009;"/>
-                </assert_contents>
-            </output>
-            <output name="proteinorthograph">
-                <assert_contents>
-                    <has_text text="E_10&#009;C_10&#009;"/>
-                </assert_contents>
-            </output>
+            <param name="p" value="blastp"/>
+            <expand macro="test_outputs"/>
+            <assert_command>
+                <has_text text="--p=blastp"/>
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[Proteinortho with POFF - An orthology detection tool
--- a/proteinortho_macros.xml	Tue Feb 18 17:57:28 2020 -0500
+++ b/proteinortho_macros.xml	Tue Sep 14 11:39:10 2021 +0000
@@ -1,7 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@TOOL_VERSION@">6.0.14</token>
-   <token name="@WRAPPER_VERSION@">2.9.1</token>
+   <token name="@TOOL_VERSION@">6.0.31</token>
+   <token name="@WRAPPER_VERSION@">0</token>
+   <token name="@PROFILE@">20.09</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-12-124</citation>
@@ -11,10 +12,12 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement>
-            <requirement type="package">diamond</requirement>
-            <requirement type="package">blast</requirement>
-            <requirement type="package">blat</requirement>
-            <requirement type="package">last</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="1256">last</requirement>
         </requirements>
     </xml>
     <xml name="version_command">