| Previous changeset 26:a2dc1e1c10db (2017-02-06) Next changeset 28:71b765a4c494 (2017-02-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'e513259f9701a68e53baddaeedfa51406df857bf\n'-dirty |
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modified:
align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml |
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| diff -r a2dc1e1c10db -r f33b89fe9f82 align_families.xml --- a/align_families.xml Mon Feb 06 23:34:30 2017 -0500 +++ b/align_families.xml Sat Feb 18 04:10:19 2017 -0500 |
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| @@ -3,11 +3,10 @@ <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="0.6">duplex</requirement> - <requirement type="set_environment">DUPLEX_DIR</requirement> + <requirement type="package" version="0.6.1">duplex</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code">python "\$DUPLEX_DIR/align_families.py" -p \${GALAXY_SLOTS:-1} '$input' > '$output' + <command detect_errors="exit_code">align_families.py -p \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
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| diff -r a2dc1e1c10db -r f33b89fe9f82 correct_barcodes.xml --- a/correct_barcodes.xml Mon Feb 06 23:34:30 2017 -0500 +++ b/correct_barcodes.xml Sat Feb 18 04:10:19 2017 -0500 |
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| @@ -5,14 +5,10 @@ <requirement type="package" version="2.1.0">bowtie2</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.9">networkx</requirement> - <requirement type="package" version="0.6">duplex</requirement> - <requirement type="set_environment">DUPLEX_DIR</requirement> + <requirement type="package" version="0.6.1">duplex</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code">bash "\$DUPLEX_DIR/baralign.sh" '$input' refdir barcodes.bam - && samtools view -f 256 barcodes.bam - | python "\$DUPLEX_DIR/correct.py" -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa - | sort > '$output' + <command detect_errors="exit_code">correct-barcodes.sh -d $dist -m $mapq -p $pos '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
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| diff -r a2dc1e1c10db -r f33b89fe9f82 dunovo.xml --- a/dunovo.xml Mon Feb 06 23:34:30 2017 -0500 +++ b/dunovo.xml Sat Feb 18 04:10:19 2017 -0500 |
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| @@ -2,21 +2,13 @@ <tool id="duplex" name="Du Novo: Make consensus reads" version="0.6"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="0.6">duplex</requirement> - <requirement type="set_environment">DUPLEX_DIR</requirement> + <requirement type="package" version="0.6.1">duplex</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' + <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2' #if $keep_sscs: - --sscs-file sscs.fa + '$sscs1' '$sscs2' #end if - > duplex.fa - && python "\$DUPLEX_DIR/utils/outconv.py" duplex.fa -1 '$dcs1' -2 '$dcs2' - #if $keep_sscs: - && python "\$DUPLEX_DIR/utils/outconv.py" sscs.fa -1 '$sscs1' -2 '$sscs2' - #end if - ]]> </command> <inputs> <param name="input" type="data" format="tabular" label="Aligned input reads" /> |
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| diff -r a2dc1e1c10db -r f33b89fe9f82 make_families.xml --- a/make_families.xml Mon Feb 06 23:34:30 2017 -0500 +++ b/make_families.xml Sat Feb 18 04:10:19 2017 -0500 |
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| @@ -2,15 +2,10 @@ <tool id="make_families" name="Du Novo: Make families" version="0.6"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="0.6">duplex</requirement> - <requirement type="set_environment">DUPLEX_DIR</requirement> + <requirement type="package" version="0.6.1">duplex</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> - <command>paste '$fastq1' '$fastq2' - | paste - - - - - | awk -f "\$DUPLEX_DIR/make-barcodes.awk" -v TAG_LEN=$taglen -v INVARIANT=$invariant - | sort - > '$output' + <command detect_errors="exit_code">make-families.sh -v TAG_LEN=$taglen -v INVARIANT=$invariant '$fastq1' '$fastq2' > '$output' </command> <inputs> <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/> |
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| diff -r a2dc1e1c10db -r f33b89fe9f82 tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 06 23:34:30 2017 -0500 +++ b/tool_dependencies.xml Sat Feb 18 04:10:19 2017 -0500 |
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| @@ -12,17 +12,16 @@ <package name="networkx" version="1.9"> <repository changeset_revision="2ca57555a756" name="package_networkx_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="duplex" version="0.6"> + <package name="duplex" version="0.6.1"> <install version="1.0"> <actions> - <action sha256sum="a3cc378c22fcfc3bcaa11129f27f61bab5ff51cc9185320d53ece273b56e6214" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.6.tar.gz</action> + <action sha256sum="f4ee6ef4db6b97bd96bcfb79b18b2ed87b933c8bbbc26073390597da84683ee0" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.6.1.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="set_environment"> - <environment_variable action="set_to" name="DUPLEX_DIR">$INSTALL_DIR</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> </action> </actions> |