changeset 1:2df37db680ad draft default tip

planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/ccqtl commit ac8fec726c224fad58f9451042f6f62f180c8c5c

--- a/ccqtl-permutations.xml	Fri Jun 30 14:18:58 2023 +0000
+++ b/ccqtl-permutations.xml	Fri Sep 29 14:58:06 2023 +0000
@@ -1,17 +1,11 @@
 <tool id="ccqtl_permutations" name="CCQTL: Run permutations" version="@TOOL_VERSION@+@WRAPPER_VERSION@" python_template_version="3.5">
     <description>to define significance thresholds</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">galaxy0</token>
+        <token name="@WRAPPER_VERSION@">galaxy1</token>
         <import>macros.xml</import>
     </macros>
-    <edam_topics>
-        <edam_topic>topic_0625</edam_topic>
-        <edam_topic>topic_0160</edam_topic>
-        <edam_topic>topic_3338</edam_topic>
-    </edam_topics>
-    <edam_operations>
-        <edam_operation>operation_3232</edam_operation>
-    </edam_operations>
+    <expand macro="edam"/>
+    <expand macro="xrefs"/>
     <requirements>
         <expand macro="requirements"/>
     </requirements>
@@ -33,7 +27,7 @@
         <expand macro="crossdata"/>
         <expand macro="clean_pr"/>
         <expand macro="kloco"/>
-        <param argument="--n_perm" type="integer" value="2" min="0" max="1000" label="Number of permutations (recommended minimum: 100)"/>
+        <param argument="--n_perm" type="integer" value="100" min="2" max="20000" label="Number of permutations (recommended minimum: 100)"/>
         <param argument="--covar_modmat" type="data" format="rds" label="covar_modmat object (rds)"/>
         <param argument="--strat_covar" type="text" value="" label="List of covariates used to stratify permutations on." help="At most three covariates, all must be categorical and previously passed as covariate at the genome_scan step. Typical stratification covariate is sex."/>
     </inputs>

--- a/macros.xml	Fri Jun 30 14:18:58 2023 +0000
+++ b/macros.xml	Fri Sep 29 14:58:06 2023 +0000
@@ -1,5 +1,20 @@
 <macros>
     <token name="@TOOL_VERSION@">0.0.1_beta.2</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">ccqtl</xref>
+        </xrefs>
+    </xml>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_0625</edam_topic>
+            <edam_topic>topic_0160</edam_topic>
+            <edam_topic>topic_3338</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_3232</edam_operation>
+        </edam_operations>
+    </xml>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">r-ccqtl</requirement>
         <yield/>
@@ -35,14 +50,14 @@
     <xml name="citations">
         <citations>
             <citation type="bibtex">
-@misc{githubseqtk,
-    author = {Victoire Baillet, Rémi Planel, Vincent Guillemot, Pascal Campagne},
-    year = {2023},
-    title = {ccqtl},
-    publisher = {Gitlab},
-    journal = {Gitlab repository},
-    url = {https://gitlab.pasteur.fr/cc-qtl/ccqtl},
-}</citation>
+                @misc{githubseqtk,
+                author = {Victoire Baillet, Rémi Planel, Vincent Guillemot, Pascal Campagne},
+                year = {2023},
+                title = {ccqtl},
+                publisher = {Gitlab},
+                journal = {Gitlab repository},
+                url = {https://gitlab.pasteur.fr/cc-qtl/ccqtl},
+                }</citation>
         </citations>
     </xml>
 </macros>