diff concoct_coverage_table.xml @ 2:6302656ed45d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concoct_coverage_table.xml	Thu Jul 07 08:32:46 2022 +0000
@@ -0,0 +1,50 @@
+<tool id="concoct_coverage_table" name="CONCOCT: Generate the input coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for CONCOCT</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.15.1">samtools</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir 'mapping' &&
+#for $e in $bamfiles
+    ln -s '$e' 'mapping/${e.element_identifier}.sorted.bam' &&
+    samtools index 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam.bai' &&
+    mv 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam' &&
+#end for
+concoct_coverage_table.py
+    '$bedfile'
+    mapping/*.bam
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param name="bedfile" type="data" format="bed" label="Contigs BEDFile" help="The file should have four columns representing: 'Contig ID, Start Position, End Position and SubContig ID' respectively. The Subcontig ID must contain the pattern 'concoct_part_[0-9]*' while the contigs which are not cutup cannot contain this pattern. This file can be generated by the cut_up_fasta tool."/>
+        <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
+            <param name="bamfiles" value="ten_reads_two_contigs-s.bam" ftype="bam"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="contig-21000001.concoct_part_0"/>
+                    <has_n_lines n="11"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
+file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
+CONCOCT metagenome binning tool.
+
+@HELP_OVERVIEW@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>