Fix autoupdate macs2 (#5453)

* Adjust param name in test 1 and 2/ Version update * fixed wrong xml order * Delete redudant names * Change r-base version to 4.3 * Adjusting macs2 version number
galaxyproject · Oct 13, 2023 · 7bd4238 · 7bd4238
1 parent 0c2ed11
commit 7bd4238
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Showing 11 changed files with 25 additions and 25 deletions.
diff --git a/tools/macs2/macs2_bdgbroadcall.xml b/tools/macs2/macs2_bdgbroadcall.xml
@@ -1,11 +1,11 @@
 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
-    <description>Call broad peaks from bedGraph output</description>
-    <expand macro="bio_tools"/>
+    <description>Call broad peaks from bedGraph output</description> 
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="4.1.3">gawk</requirement>
+        <requirement type="package" version="5.1.0">gawk</requirement>
     </expand>
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_bdgcmp.xml b/tools/macs2/macs2_bdgcmp.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Deduct noise by comparing two signal tracks in bedGraph</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_bdgdiff.xml b/tools/macs2/macs2_bdgdiff.xml
@@ -1,11 +1,11 @@
 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Differential peak detection based on paired four bedgraph files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="4.1.3">gawk</requirement>
+        <requirement type="package" version="5.1.0">gawk</requirement>
     </expand>
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_bdgpeakcall.xml b/tools/macs2/macs2_bdgpeakcall.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
-    <description>Call peaks from bedGraph output</description>
-    <expand macro="bio_tools"/>
+    <description>Call peaks from bedGraph output</description> 
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_callpeak.xml b/tools/macs2/macs2_callpeak.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
-    <description>Call peaks from alignment results</description>
-    <expand macro="bio_tools"/>
+    <description>Call peaks from alignment results</description> 
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
     </expand>
     <expand macro="stdio" />
@@ -218,7 +218,7 @@
         </param>
 
         <section name="advanced_options" title="Advanced Options">
-                <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
+                <param argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
                     label="When set, scale the small sample up to the bigger sample"
                     help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
                 <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
@@ -244,7 +244,7 @@
                             help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                     </when>
                     <when value="nobroad">
-                        <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
+                        <param argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
                             label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
                     </when>
                 </conditional>
@@ -313,8 +313,8 @@
             <param name="outputs" value="peaks_tabular,bdg,html"/>
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
-            <param name="lower" value="5" />
-            <param name="upper" value="50" />
+            <param name="mfold_lower" value="5" />
+            <param name="mfold_upper" value="50" />
             <assert_command>
                 <has_text text="--buffer-size"/>
                 <has_text text="--d-min"/>
@@ -340,8 +340,8 @@
             <param name="outputs" value="pdf"/>
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
-            <param name="lower" value="5" />
-            <param name="upper" value="50" />
+            <param name="mfold_lower" value="5" />
+            <param name="mfold_upper" value="50" />
             <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <!-- Ensure BAMPE works -->

diff --git a/tools/macs2/macs2_filterdup.xml b/tools/macs2/macs2_filterdup.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Remove duplicate reads at the same position</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_macros.xml b/tools/macs2/macs2_macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.7.1</token>
+    <token name="@TOOL_VERSION@">2.2.9.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">macs2</requirement>
-            <requirement type="package" version="3.4">r-base</requirement>
+            <requirement type="package" version="4.3">r-base</requirement>
             <yield />
         </requirements>
     </xml>

diff --git a/tools/macs2/macs2_predictd.xml b/tools/macs2/macs2_predictd.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Predict 'd' or fragment size from alignment results</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_randsample.xml b/tools/macs2/macs2_randsample.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_randsample" name="MACS2 randsample" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
-    <description>Randomly sample number or percentage of total reads</description>
-    <expand macro="bio_tools"/>
+    <description>Randomly sample number or percentage of total reads</description> 
     <macros>
-        <import>macs2_macros.xml</import>
+	    <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/macs2_refinepeak.xml b/tools/macs2/macs2_refinepeak.xml
@@ -1,9 +1,9 @@
 <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />

diff --git a/tools/macs2/test-data/callpeak_part.tabular b/tools/macs2/test-data/callpeak_part.tabular
@@ -1,4 +1,4 @@
-# This file is generated by MACS version 2.2.7.1
+# This file is generated by MACS version 2.2.9.1
 # Command line: callpeak -t /tmp/tmpnaqc0336/files/3/f/0/dataset_3f02f858-205a-41bb-bfbc-712b99093ecb.dat --name ChIP_200K_bed -c /tmp/tmpnaqc0336/files/e/4/5/dataset_e45de785-43dc-44da-badd-fd49fc164b85.dat --format BED --gsize 3300000000 --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300
 # ARGUMENTS LIST:
 # name = ChIP_200K_bed