| Previous changeset 7:366a11d316a7 (2022-05-31) Next changeset 9:c388a21dcbf1 (2023-01-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed |
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modified:
hifiasm.xml |
| b |
| diff -r 366a11d316a7 -r 5f625c63b8bc hifiasm.xml --- a/hifiasm.xml Tue May 31 14:15:45 2022 +0000 +++ b/hifiasm.xml Tue Oct 25 18:13:16 2022 +0000 |
| b |
| @@ -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" /> |