diff picrust2_pathways_macros.xml @ 0:7275d6a514d2 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picrust2_pathways_macros.xml	Wed Jan 28 16:20:19 2026 +0000
@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@PICRUST2_PATHWAYS_CMD_LINE@">
+        frogsfunc_pathways.py
+            @CPUS@
+            --input-tsv '$input_tsv'
+            --map $database.fields.path
+
+          #if $normalisation
+            --normalisation
+          #end if
+
+          --html $html
+          --output-pathways-abund '$output_pathways_abund'
+    </token>
+
+    <xml name="picrust2_pathways_inputs">
+        <!-- Files -->
+        <param argument="--input-tsv" format="tsv" type="data" label="Function abundance file (format Tsv)" help="Function TSV abundance (output of picrust2_functions tool : EC_unstrat_abundance.tsv or KO_unstrat_abundance.tsv)." optional="false"/>
+
+        <!-- References -->
+        <param name="marker" type="select" multiple="false" display="radio" label="Marker gene" help="Marker gene analysed.">
+            <options from_data_table="frogs_picrust2_pathways">
+                <column name='name' index='2' />
+                <column name='value' index='2' />
+                <filter type="unique_value" column='2'/>
+                    <validator type="no_options" message="A built-in database is not available" />
+            </options>
+        </param>
+        <param name="database" type='select' label="Pathway reference database" help="For 16S marker, choose Metacyc (EC functions) or KEGG (KO functions) in accordance with your function abundance input file. For fungi ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'>
+            <options from_data_table="frogs_picrust2_pathways">
+                <column name='name' index='1'/>
+                <column name='value' index='1'/>
+                <column name='path' index='3'/>
+                <filter type="param_value" ref="marker" column="2" />               
+                <validator type="no_options" message="A built-in database is not available" />
+            </options>
+        </param>
+
+        <!-- Parameters-->
+        <param argument="--normalisation" label="Do you want to normalize the final output table ?" help='Values are divided by sum of columns, then multiplied by 10^6 (CPM values).' type="boolean" />
+    </xml>
+
+    <!-- Test -->
+    <xml name="picrust2_pathways_test_input">
+        <param name="input_tsv" value="references/26-frogsfunc_functions_unstrat_EC.tsv" />
+        <param name="marker" value="16S" />
+        <param name="database" value="Metacyc" />
+    </xml>
+
+    <xml name="picrust2_pathways_test_output">
+        <output name="output_pathways_abund" file="references/27-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
+        <output name="html" file="references/27-frogsfunc_pathways_summary.html" compare="diff" lines_diff="0" />
+    </xml>       
+</macros>
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