diff filter_contigs.xml @ 0:222fb7dc2286 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_contigs.xml	Fri Jan 06 15:52:31 2023 +0000
@@ -0,0 +1,52 @@
+<tool id="filter_contigs" name="Filter contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description>from an assembled FASTA file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#if $input.is_of_type('fasta.gz'):
+    gunzip -c '$input' > 'input.fasta' &&
+#else:
+    ln -s '$input' 'input.fasta' &&
+#end if
+faidx -i chromsizes 'input.fasta' | awk '($2 <= $max_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/>
+        <param name="max_len" type="integer" value="1500000" min="0" label="Maximum contig length"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.fasta.gz" ftype="fasta.gz"/>
+            <param name="max_len" value="30000"/>
+            <output name="output" ftype="fasta">
+                <assert_contents>
+                    <has_size value="51690"/>
+                    <has_text text=">contig_10"/>
+                    <has_text text=">contig_7"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="input2.fasta" ftype="fasta"/>
+            <param name="max_len" value="30000"/>
+            <output name="output" ftype="fasta">
+                <assert_contents>
+                    <has_size value="28492"/>
+                    <has_text text=">contig_7"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Filters contigs from an assembled fasta file that are longer than the specified length.
+    </help>
+    <expand macro="citations"/>
+</tool>
+