Mercurial > repos > bgruening > hifiasm

changeset 7:366a11d316a7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
author bgruening
date Tue, 31 May 2022 14:15:45 +0000
parents 5bec28269d95
children 5f625c63b8bc
files hifiasm.xml
diffstat 1 files changed, 11 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/hifiasm.xml	Sat Feb 12 17:15:48 2022 +0000
+++ b/hifiasm.xml	Tue May 31 14:15:45 2022 +0000
@@ -2,7 +2,7 @@
     <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
     <macros>
         <token name="@TOOL_VERSION@">0.16.1</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
         <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
         <xml name="reads">
             <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
@@ -278,6 +278,9 @@
         <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
             <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
         </data>
+        <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
+            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
+        </data>
         <!--Trio outputs with Hi-c reads-->
         <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
             <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
@@ -338,7 +341,7 @@
             </output>
         </test>
         <!--Test Hi-C reads-->
-        <test expect_num_outputs="4"> 
+        <test expect_num_outputs="5"> 
             <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
             <param name="filter_bits" value="0" />
             <param name="mode_selector" value="standard" />
@@ -365,6 +368,12 @@
                     <has_size value="59529" delta="500"/>
                 </assert_contents>
             </output>
+            <output name="hic_raw_initig" ftype="gfa1" >
+                <assert_contents>
+                    <has_text_matching expression="^S" />
+                    <has_size value="59522" delta="500"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test trio mode -->
         <test expect_num_outputs="4">