Mercurial > repos > iuc > genebed_maf_to_fasta

diff macros.xml @ 0:f24a9ff28d3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
author iuc
date Fri, 21 Aug 2020 15:10:13 -0400
parents
children 020c78e91cc5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Aug 21 15:10:13 2020 -0400
@@ -0,0 +1,51 @@
+<macros>
+    <xml name="requirements">
+        <requirement type="package" version="0.8.9">bx-python</requirement>
+        <yield />
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr398</citation>
+        </citations>
+    </xml>
+    <xml name="maf_source">
+        <conditional name="maf_source_type">
+            <param name="maf_source" type="select" label="MAF Source">
+                <option value="cached" selected="true">Locally Cached Alignments</option>
+                <option value="user">Alignments in Your History</option>
+            </param>
+            <when value="user">
+                <param format="maf" name="maf_file" label="Choose alignments" type="data">
+                    <options>
+                        <filter type="data_meta" ref="input1" key="dbkey" />
+                    </options>
+                    <validator type="dataset_ok_validator" />
+                </param>
+                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
+                    <options>
+                        <filter type="data_meta" ref="maf_file" key="species" />
+                    </options>
+                </param>
+            </when>
+            <when value="cached">
+                <param name="mafType" type="select" label="Choose alignments">
+                    <options from_data_table="maf_indexes">
+                        <column name="name" index="0"/>
+                        <column name="value" index="1"/>
+                        <column name="indexed_for" index="2"/>
+                        <column name="exists_in_maf" index="3" />
+                        <column name="path" index="4" />
+                        <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
+                        <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
+                    </options>
+                </param>
+                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
+                    <options from_data_table="maf_indexes">
+                        <column name="value" index="3"/>
+                        <filter type="multiple_splitter" column="3" separator=","/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+</macros>