| Previous changeset 4:7f513b9b1b1e (2015-12-21) Next changeset 6:9a0bee12b583 (2017-02-06) |
|
Commit message:
Version 0.5: Split interleaved SSCS output file into two paired files. |
|
modified:
align_families.xml dunovo.xml make_families.xml tool_dependencies.xml |
| b |
| diff -r 7f513b9b1b1e -r 4bc49a5769ee align_families.xml --- a/align_families.xml Mon Dec 21 14:47:48 2015 -0500 +++ b/align_families.xml Thu Dec 01 23:22:52 2016 -0500 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="0.3"> +<tool id="align_families" name="Du Novo: Align families" version="0.5"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="0.3">duplex</requirement> + <requirement type="package" version="0.5">duplex</requirement> <requirement type="set_environment">DUPLEX_DIR</requirement> <!-- TODO: require Python 2.7 --> </requirements> |
| b |
| diff -r 7f513b9b1b1e -r 4bc49a5769ee dunovo.xml --- a/dunovo.xml Mon Dec 21 14:47:48 2015 -0500 +++ b/dunovo.xml Thu Dec 01 23:22:52 2016 -0500 |
| [ |
| @@ -1,19 +1,21 @@ <?xml version="1.0"?> -<tool id="duplex" name="Du Novo: Make consensus reads" version="0.3"> +<tool id="duplex" name="Du Novo: Make consensus reads" version="0.5"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="0.3">duplex</requirement> + <requirement type="package" version="0.5">duplex</requirement> <requirement type="set_environment">DUPLEX_DIR</requirement> <!-- TODO: require Python 2.7 --> </requirements> <command detect_errors="exit_code"><![CDATA[ python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input #if $keep_sscs: - --sscs-file $sscs + --sscs-file sscs.fa #end if > duplex.fa - && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1 - && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2 + && python \$DUPLEX_DIR/utils/outconv.py duplex.fa -1 $dcs1 -2 $dcs2 + #if $keep_sscs: + && python \$DUPLEX_DIR/utils/outconv.py sscs.fa -1 $sscs1 -2 $sscs2 + #end if ]]> </command> <inputs> @@ -24,20 +26,23 @@ <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> <option value="solexa">Solexa (PHRED 0 = "@")</option> </param> - <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" /> + <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> </inputs> <outputs> - <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/> - <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/> - <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)"> + <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> + <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> + <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> + <filter>keep_sscs</filter> + </data> + <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)"> <filter>keep_sscs</filter> </data> </outputs> <tests> <test> <param name="input" value="families.msa.tsv"/> - <output name="output1" file="families.cons_1.fa"/> - <output name="output2" file="families.cons_2.fa"/> + <output name="dcs1" file="families.cons_1.fa"/> + <output name="dcs2" file="families.cons_2.fa"/> </test> </tests> <help> |
| b |
| diff -r 7f513b9b1b1e -r 4bc49a5769ee make_families.xml --- a/make_families.xml Mon Dec 21 14:47:48 2015 -0500 +++ b/make_families.xml Thu Dec 01 23:22:52 2016 -0500 |
| b |
| @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="0.3"> +<tool id="make_families" name="Du Novo: Make families" version="0.5"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="0.3">duplex</requirement> + <requirement type="package" version="0.5">duplex</requirement> <requirement type="set_environment">DUPLEX_DIR</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> |
| b |
| diff -r 7f513b9b1b1e -r 4bc49a5769ee tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 21 14:47:48 2015 -0500 +++ b/tool_dependencies.xml Thu Dec 01 23:22:52 2016 -0500 |
| b |
| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="mafft" version="7.221"> - <repository changeset_revision="d71e007323d4" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="15974dd17515" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="duplex" version="0.3"> + <package name="duplex" version="0.5"> <install version="1.0"> <actions> - <action type="download_by_url">https://github.com/makrutenko/dunovo/archive/v0.3.tar.gz</action> + <action type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.5.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory> |