diff Fasta_to_Contig2Bin.xml @ 0:5033d753964b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Fasta_to_Contig2Bin.xml	Mon Jun 27 12:41:53 2022 +0000
@@ -0,0 +1,52 @@
+<tool id="Fasta_to_Contig2Bin" name="Converts genome bins in fasta format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        to scaffolds-to-bin table
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+mkdir "inputs" &&
+#for $i in $inputs
+    #set file_name = $i.file_name
+    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+    ln -s '$file_name' 'inputs/${identifier}.fasta' &&
+#end for
+Fasta_to_Contig2Bin.sh
+    --extension fasta
+    --input_folder 'inputs'
+    > '$contigs2bin'
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data_collection" collection_type="list"  format="fasta" label="Bin sequences"/>
+    </inputs>
+    <outputs>
+        <data name="contigs2bin" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="inputs">
+                <collection type="list">
+                    <element name="001" value="maxbin2.001.fasta" ftype="fasta"/>
+                    <element name="002" value="maxbin2.002.fasta" ftype="fasta"/>
+                </collection>
+            </param>
+            <output name="contigs2bin" ftype="tabular">
+                <assert_contents>
+                    <has_text text="contig-201_2"/>
+                    <has_text text="001"/>
+                    <has_text text="contig-201_798"/>
+                    <has_text text="002"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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