diff macros.xml @ 0:6b6c9ab21674 draft

planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/ccqtl commit 320b3741bd00d1707829822302abe0f0b610981a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jun 30 14:18:58 2023 +0000
@@ -0,0 +1,48 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.0.1_beta.2</token>
+    <xml name="requirements">
+        <requirement type="package" version="@TOOL_VERSION@">r-ccqtl</requirement>
+        <yield/>
+    </xml>
+    <token name="@BASE_CMD@">
+        ccqtl --cores \${GALAXY_SLOTS:-1}
+    </token>
+    <xml name="indiv_marker">
+        <param name="indiv_marker" argument="--indiv_geno" type="select" label="Select individual genotypes of each CC mouse at each marker" help="Directory that contains the individual genotypes of each CC mouse at each marker and the funnel codes if applicable.">
+            <options from_data_table="ccqtl">
+                <filter type="static_value" column="1" value="indiv_marker"/>
+                <validator type="no_options" message="No dataset available for the selected input dataset"/>
+            </options>
+        </param>
+    </xml>
+    <xml name="marker_set">
+        <param argument="--marker_set" type="select" label="Select the genetic and physical maps as well as the founder genotypes information" help="Directory that contains the genetic and physical maps as well as the founder genotypes information, for the different combinations of marker set and genome build.">
+            <options from_data_table="ccqtl">
+                <filter type="static_value" column="1" value="marker_set"/>
+                <validator type="no_options" message="No dataset available for the selected input dataset"/>
+            </options>
+        </param>
+    </xml>
+    <xml name="crossdata">
+        <param argument="--crossdata" type="data" format="rds" label="crossdata rds file" help="The cross rds file output from make_inputs"/>
+    </xml>
+    <xml name="kloco">
+        <param argument="--kloco" type="data" format="rds" label="kloco rds file" help="the LOCO kinship rds file output from make_inputs"/>
+    </xml>
+    <xml name="clean_pr">
+        <param argument="--clean_pr" type="data" format="rds" label="clean_pr ds file" help="The cleaned genotype probabilities rds file output from make_inputs"/>
+    </xml>
+    <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>
+        </citations>
+    </xml>
+</macros>