diff coverm_contig.xml @ 4:1dcea261abbe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5

--- a/coverm_contig.xml	Wed Jul 26 07:35:24 2023 +0000
+++ b/coverm_contig.xml	Fri Aug 18 09:23:21 2023 +0000
@@ -231,6 +231,51 @@
             <conditional name="mapped">
                 <param name="mapped" value="not-mapped" />
                 <conditional name="mode">
+                    <param name="mode" value="individual"/>
+                    <conditional name="read_type">
+                        <param name="type" value="paired_collection"/>
+                        <param name="paired_reads">
+                            <collection type="paired">
+                                <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </param>
+                    </conditional>
+                    <param name="reference" value="7seqs.fna" />
+                    <param name="sharded" value="" />
+                </conditional>
+            </conditional>
+            <section name="alignment">
+                <param name="min_read_aligned_length" value="0" />
+                <param name="min_read_percent_identity" value="0" />
+                <param name="min_read_aligned_percent" value="0" />
+                <conditional name="proper_pairs_only">
+                    <param name="proper_pairs_only" value=""/>
+                </conditional>
+                <param name="exclude_supplementary" value=""/>
+            </section>
+            <section name="cov">
+                <param name="methods" value="mean"/>
+                <param name="trim_min" value="5"/>
+                <param name="trim_max" value="95"/>
+                <param name="min_covered_fraction" value="10"/>
+                <param name="contig_end_exclusion" value="75"/>
+            </section>
+            <param name="output_format" value="dense"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Contig"/>
+                    <has_text text="Mean"/>
+                    <has_text text="7seqs.fna"/>
+                    <has_text text="genome1~random_sequence_length_11000"/>
+                    <has_text text="genome2~seq1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mapped">
+                <param name="mapped" value="not-mapped" />
+                <conditional name="mode">
                     <param name="mode" value="co"/>
                     <conditional name="read_type">
                         <param name="type" value="single"/>