diff catWrapper.xml @ 0:6f54dc6b37da draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/catWrapper.xml	Sun Mar 11 18:19:40 2018 -0400
@@ -0,0 +1,89 @@
+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="0.3">
+    <description>tail-to-head</description>
+    <command><![CDATA[
+        #if $headers == "No":
+            cat
+            #for $file in $input
+                "$file"
+            #end for
+            > "$out_file1"
+        #else:
+            #for $file in $input
+                printf "# ${file.element_identifier}\n" >> "$out_file1" &&
+                cat "$file" >> "$out_file1" &&
+            #end for
+            sleep 1
+        #end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="headers" type="select" label="include dataset names">
+                <option value="No" selected="true">No</option>
+                <option value="Yes">Yes</option>
+        </param>
+        <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="headers" value="No" />
+            <param name="input" value="1.bed,2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out1.bed"/>
+        </test>
+        <test>
+            <param name="headers" value="Yes" />
+            <param name="input" value="1.bed,2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out2.bed"/>
+        </test>
+
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+**WARNING:** This tool does not check if the datasets being concatenated are in the same format.
+
+-----
+
+**What it does**
+
+Concatenates datasets
+
+-----
+
+**Example**
+
+Concatenating Dataset::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+
+with Dataset1::
+
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+and with Dataset2::
+
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+
+will result in the following::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+    chr2  100000030  200000955  P  0  +
+    chr2  100000015  200000999  Q  0  +
+
+-----
+
+Adapted from galaxy's catWrapper.xml to allow multiple input files.
+
+    </help>
+</tool>