Mercurial > repos > bgruening > hifiasm

changeset 8:5f625c63b8bc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
author bgruening
date Tue, 25 Oct 2022 18:13:16 +0000
parents 366a11d316a7
children c388a21dcbf1
files hifiasm.xml
diffstat 1 files changed, 16 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/hifiasm.xml	Tue May 31 14:15:45 2022 +0000
+++ b/hifiasm.xml	Tue Oct 25 18:13:16 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@">3</token>
+        <token name="@VERSION_SUFFIX@">4</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" />
@@ -131,6 +131,7 @@
         #if $log_out:
             2> output.log
         #end if
+	    && mkdir noseq_files && mv *.noseq.gfa noseq_files
         ]]>
     </command>
     <inputs>
@@ -292,9 +293,12 @@
         <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
             <filter>log_out</filter>
         </data>
+        <collection name="noseq files" type="list" label="${tool.name} on ${on_string}: noseq files">
+            <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
+        </collection>
     </outputs>
     <tests>
-        <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" />
@@ -307,7 +311,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
             <param name="filter_bits" value="0" />
             <param name="mode_selector" value="standard" />
@@ -321,7 +325,7 @@
             </output>
         </test>
         <!-- Test logfile out-->
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="6">
             <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
             <param name="filter_bits" value="0" />
             <param name="mode_selector" value="standard" />
@@ -341,7 +345,7 @@
             </output>
         </test>
         <!--Test Hi-C reads-->
-        <test expect_num_outputs="5"> 
+        <test expect_num_outputs="6"> 
             <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
             <param name="filter_bits" value="0" />
             <param name="mode_selector" value="standard" />
@@ -376,7 +380,7 @@
             </output>
         </test>
         <!-- Test trio mode -->
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="filter_bits" value="0"/>
             <conditional name="mode">
                 <param name="mode_selector" value="trio"/>
@@ -408,7 +412,7 @@
             </output>
         </test>
         <!-- Test ignore-error-corrected option -->
-        <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" />
@@ -426,7 +430,7 @@
             </output>
         </test>
         <!-- Test expected haplotype number -->
-        <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" />
@@ -444,7 +448,7 @@
             </output>
         </test>
         <!-- Test min_hist_cnt option -->
-        <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" />
@@ -462,7 +466,7 @@
             </output>
         </test>
         <!-- Test max_kooc option -->
-        <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" />
@@ -480,7 +484,7 @@
             </output>
         </test>
         <!-- Test hg-size option -->
-        <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" />
@@ -498,7 +502,7 @@
             </output>
         </test>
         <!-- Test ignore-error-corrected option -->
-        <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" />