diff macros.xml @ 0:9d593c42f037 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Nov 04 12:26:56 2025 +0000
@@ -0,0 +1,101 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
+            <requirement type="package" version="1.22">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">2.1.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
+
+    <xml name="optional_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="no">No</option>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="no"/>
+            <when value="history">
+                <param argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey"/>
+                    </options>
+                    <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="mandatory_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="history">
+                <param argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey"/>
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
+        #set use_ref=True
+        #if $addref_cond.addref_select == "history":
+            #if $addref_cond.ref.is_of_type('fasta'):
+                reffa="reference.fa" &&
+                ln -s '${addref_cond.ref}' \$reffa &&
+                samtools faidx \$reffa &&
+            #else:
+                reffa="reference.fa.gz" &&
+                ln -s '${addref_cond.ref}' \$reffa &&
+                {
+                    samtools faidx \$reffa ||
+                    {
+                        echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
+                        gzip -dc \$reffa > reference.fa &&
+                        reffa="reference.fa" &&
+                        samtools faidx \$reffa;
+                    }
+                } &&
+            #end if
+            reffai=\$reffa.fai &&
+        #elif $addref_cond.addref_select == "cached":
+            reffa='${addref_cond.ref.fields.path}' &&
+            reffai=\$reffa.fai &&
+        #else
+            #set use_ref=False
+        #end if
+    ]]></token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.16878970</citation>
+        </citations>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[fgbio --version 2>&1 | grep Version]]></version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+</macros>