diff merge_ampvis2.xml @ 0:028ba7c0b400 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_ampvis2.xml	Thu Apr 07 14:07:36 2022 +0000
@@ -0,0 +1,78 @@
+<tool id="ampvis2_merge_ampvis2" name="ampvis2 merge ampvis2 data sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="header"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$rscript'
+    ]]></command>
+    <configfiles>
+        <configfile name="rscript"><![CDATA[
+            library(ampvis2, quietly = TRUE)
+            merged <- amp_merge_ampvis2(
+            #for d in $data
+                readRDS("$d"), 
+            #end for
+            by_refseq = $by_refseq
+            )
+            saveRDS(merged, "$output")
+            merged
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_input_macro" multiple="true"/>
+        <param argument="by_refseq" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Merge by exact matches between DNA reference sequences" help="The full DNA sequences will then be used as the new names in the output."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="ampvis2"/>
+    </outputs>
+    <tests>
+        <!-- defaults -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.2010.rds,AalborgWWTPs.2011.rds" ftype="ampvis2"/> 
+            <output name="output" ftype="ampvis2">
+                <assert_contents>
+                    <has_size value="70888" delta="1000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <!--check that the merged data has 13 samples-->
+                <has_text text="13          125         6714          193         1019          475"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Merge any number of ampvis2 data sets into a single data set.
+
+The Galaxy tool calls the `amp_merge_ampvis2
+<https://madsalbertsen.github.io/ampvis2/reference/amp_merge_ampvis2.html>`_ function
+of the ampvis2 package.
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+Details
+=======
+
+It's important to ensure that the taxonomy for all OTU's across data sets is
+generated in the exact same way with the same database. When **Merge by exact matches between DNA reference sequences** is not checked
+it's likewise important to ensure that OTU ID's are not arbitrary between data
+sets and that they are corresponding to the same sequences across data sets
+(objects). When **Merge by exact matches between DNA reference sequences** is checked the full DNA sequences will be used as the new
+OTU ID's. 
+
+Currently, phylogenetic trees are not merged.
+
+Output
+======
+
+The merged data set
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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