| Previous changeset 53:5eb0ec276ea5 (2019-06-13) Next changeset 55:5c96f12f837d (2019-07-28) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920 |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml filter_insertions.xml findcluster.xml plot_coverage.xml tool_data_table_conf.xml.sample update_mapq.xml write_supplementary_fastq.xml |
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added:
all_fasta.loc.sample extract_variants.xml test-data/all_fasta.loc test-data/long_insert_tagged.bam test-data/long_insertion.bam test-data/transposon.fa tool_data_table_conf.xml.test |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be add_matesequence.xml --- a/add_matesequence.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/add_matesequence.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.1"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.2"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be allow_dovetailing.xml --- a/allow_dovetailing.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/allow_dovetailing.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.1"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.2"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be bam_readtagger.xml --- a/bam_readtagger.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/bam_readtagger.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.1"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.2"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be extract_variants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_variants.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -0,0 +1,37 @@ +<tool id="extract_variants" name="Extract variant fragments" version="0.5.1"> + <description>from long reads</description> + <requirements> + <requirement type="package" version="0.5.1">readtagger</requirement> + </requirements> + <version_command>extract_variants --version</version_command> + <command detect_errors="aggressive"><![CDATA[ +ln -fs '$insert_reference.fields.path' reference.fa && +extract_variants '$input' '$output' reference.fa + ]]></command> + <inputs> + <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> + <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> + <options from_data_table="all_fasta"/> + </param> + </inputs> + <outputs> + <data name="output" format_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="long_insertion.bam" ftype="bam"/> + <param name="insert_reference" value="transposon"/> + <output name="output" file="long_insert_tagged.bam" ftype="bam"/> + </test> + </tests> + <help><![CDATA[ + +Extract variants will find soft-clipped alignments and alignments with insertions, +and, if the inserted sequence aligns with the selected reference, write out +a the alignment, but clip the aligned portion of the read to a single N +and will add 2 tags, AR and AD to the alignment. +The AR tag will list the contig, the AD tag contains detailed +information on how the insert/clipped sequence aligned against the selected +reference. + ]]></help> +</tool> |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be filter_insertions.xml --- a/filter_insertions.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/filter_insertions.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.1"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.2"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be findcluster.xml --- a/findcluster.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/findcluster.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.1"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.2"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be plot_coverage.xml --- a/plot_coverage.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/plot_coverage.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.1"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.2"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -0,0 +1,1 @@ +transposon transposon transposon ${__HERE__}/transposon.fa |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/long_insert_tagged.bam |
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| Binary file test-data/long_insert_tagged.bam has changed |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/long_insertion.bam |
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| Binary file test-data/long_insertion.bam has changed |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/transposon.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transposon.fa Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -0,0 +1,80 @@ +>F-element +AATCAATTAATCAATTCGATCGCCGACGTGTGAAGACGTTTTTATCGTGCTCCGCACAAA +ATCGGTTGTTTTGAGTGAAGTGAACGCCAAATAAAATAAACTAAATAAAAAATCTGAAAG +CGAAAGAGACGCTCTATGCGATGCAAGATCGCTTAAATACATAGTGAATTGTTATCTTAA +ATAATAAAACTATGAGTCAGAATGACACTCGCGCCCAGCGTCAGCGCGAGCATGACGAAC +GCCGACTCTCAATTCAGCGCAACAACGCGTACTTCTCCTACGTCTCACCGACAATCCCAA +ACGCAGACATCGAGCGGTCAATAACCCATAGCCCAGGAAACCTTCTTCTACCAACAAATC +AAGAAAGAGCGCGCTCCTGCTCTCCCGCTCTATTGGCTCCGACAGAAGCCCCGCTACCTC +CAACAACAACAGCTGGAGAGGGACCGGCAGCCCGCTCTGCCTCGTCATCGGCTGCACCCG +CTCACGGTCTGACTAAGTCAGCGAAAGCAAAACCGCTAGCAATAAACGGTACTGCTGCAC +TGCCAGCAAAACAAAACGAAAACGTAAACAAAAAAGCTGGGTCGACCTGGCAGACTGGAA +TGGACCGCTACATTACAATAAAGCGAAAGCTCAGCCCGGAAAATTCAGATTTGGGAAACA +AGCCGAAAAATACACGCGATAACTCTACCTTGATCAAAAATGTAGCCCCTGCAAATACCA +ACAGATTTGCCTTGCTGGTAGATACCGCTGAGGACGTGCCGCTGGGATCCGTTGATATCG +AACCGAAGAAAACAAAGCCTCCGCCAATATACATCCGCGAGAAGAGCACAAGCCGTCTTG +TAAATACTTTGATTGGCCTTATTGGGAAAGATAGCTTTCATATAATTCCCCTCGTAAGAG +GTACTATCAACGAAATCAAACTTCAGACGAAAACGGAGGACGACTACAGAAAAGTCACAA +ACTATTTTACCGCACAAAAAATAGGCTTCTACACCTACCAGCTTAAAAGCAGCAAGGGCC +TGCAAGTAGTCCTGAAGGGCATTGAGTCTGATGTTACGCCCGAAGAGATAACTGAGGCGC +TAAAGGAAAAGGGATTTTACGCCAAAAACGTGTTCAATATCAAAAACAGAAACAGGCAGC +CCCAACCACTCTTCAAGATTGAGCTTGAACCAGAAAACAAGCCTCCTAGAAAAAACGAGG +TTCACCCAATTTACAAACTCCAGCTCCTTTTGCACCGTAGGATCACGGTAGAAGAGCCGC +ACAAACGCAACGCTCCTGTACAATGTACAAACTGCCAAGAGTATGGCCACACGAGGTCAT +ATTGTACACTTCGCCCGGTGTGCGTAGTCTGTGGAGATCTCCACGACTCCAAACAGTGTC +AAATTAACAAAGAAAATGCATGCGAGAAAAAATGTAATAACTGCGGGGGCAATCACACAG +CAAACTACAGAGGCTGTCCAATCTACAAAGAGCTGAAAATCCGTCTTCACAAAAGAATGA +ACACGGCGCGGGCACACCAAGGATCAGCTACCCTGATACCATCAGAGACAAATCCTGAAG +TAATTTTCTCGAAAGCAGCTAGTTTCGCTCCCTGGCCTACATTCAACACTAACAAGACAA +CATTTGCTAACGTTTTAAAATCAGGTATGACGCCTCCAACCCAAAACTCCCGAACTCCAC +ATGAAGTGCACACAAAATTAGACACACAACAAAACTATCACCCAGCTGCGCAGCAGGAAA +CAAAAACTGAAGCTATGATGCAAGCCTTACAACAGAGCATGATGGAATTTATGACATTTA +TGAAGACCACCATTCAAGACATGATGCGTAATCAAAACCTTTTGATACAAATGCTTGTAG +CCCAACAATCAAATAAATAATGGCTACCTTACGCATAGCTACGTGGAACGCCAATGGCGT +CTCACAGCGCAAACTTGAGCTAGCTCAATTCCTACATGAGAAGCATATCGACGTAATGCT +TCTTTCGGAAACTCATCTCACAAGCAAATACAATTTTCAAATAAGAGACTACCATTTCTA +CGGTACAAATCATCCCGACGGAAAAGCACACGGTGGCACCGCCATACTCATAAGGAACCG +TATGAAGCACCACTTTTACAAAGAATTTGCGGAAAATCATCTTCAGGCCACATCTATCAA +CATTCAGCTGGATGACAACACTCTCCTTACACTAGCGGCCGTATACTGCCCCCCCCGTTT +CACAGTATTAGAAGCTCAATTCCTGGATTTCTTCCAAGCACTAGGGCCACACTTCATTGC +AGCAGGCGACTACAACGCTAAACATACTCACTGGGGATCGCGACTTGTGAACCCAAAAGG +AAAACAGCTTTATAAGACGATAATAAAAGCCACTAATAAACTTGACCATGTTTCCCCCGG +GAGTCCTACATACTGGCCATCAGACCTCAATAAGCTGCCAGACCTGATCGACTTCGCAGT +TACGAAAAATATTTCCCGCAGTTTGGTTAAAGCTGAATGTCTGCCGGATCTCTCATCTGA +TCACTCGCCTGTACTAATTCACCTCCGCCGATACGCAGAAAACGTGAAACCACCAACCAG +ATTGACCTCTAGCAAAACAAACTGGCTCAGGTATAAAAAATATATAAGTTCACATATTGA +GCTAAGCCCAAAACTCAATACTGAATCTGATATAGAGAGCTGCACGTGTGCATTGCAATC +CATCCTTACTGCAGCAGCTCTTACTGCAACACCCAAAATAACAAATAATACAATTAATTC +AAAAAAGACCAACGTACAAATCGAGCAACTCGTCCACGTAAAACGTCGCTTACGCAGAGA +ATGGCAATCTTCCAGATCCCCAACTGCAAAACAAAAGCTAAAAGTAGCCACACGGAAACT +GGCCAACGCTCTGAAACAAGAAGAGGACGACGATCAGCGCCGATACATAGAGCAACTCAC +ACCAACAGGCACAAAACAAAAGTCACTGTGGCGAGCCCACTCAACTCTTCGCCCACCGAC +TGAAACCGTTTTGCCGATAAGGAATTCATCAGGTGGCTGGGCCCGTAGTGATGAAGACAG +AGCCAACACATTTGCCGCTCACCTACAAAATGTGTTCACGCCAAACCAGGCTACTAGCAC +ATTCGCGCTACCGTCCTATCCCGTAAACCGCCATCAGCAACACACCCCAATTGTGTTTCG +TCCTAAAGAAATAACTAAAATAATCAAAGACAATCTCAGCCCGAAAAAATCCCCCGGCTA +CGACCTTATAACACCGGAAATGATCATCCAGCTGCCACATTCTGCAGTTCGCTACATAAC +CAAGCTCTTTAATGCCATCACCAAACTTGGTTACTTTCCACAACGATGGAAGATGATGAA +GATCATAATGATTCCAAAGCCTGGTAAGAACCACACAGTCGCTTCATCTTACAGACCAAT +AAGTCTACTCTCATGCATTTCGAAACTATTCGAAAAATGCCTGCTGATCCGACTTAATCA +ACATCTGATATACCACAATATAATCCCAGCCCACCAATTTGGATTTCGCGAAAGCCACGG +AACCATTGAACAGGTGAATCGTATTACAACGGAAATAAGAACTGCATTTGAATATCGCGA +ATACTGTACAGCAGTATTTTTAGACGTATCCCAAGCATTCGACAAAGTCTGGCTCGACGG +CCTAATGTTTAAAATTAAAACATCCCTACCCGAAAGCACACACAAACTTCTAAAGTCTTA +CCTCTATGACAGAAAGTTTGCAGTGCGGTGCAACACTGCCACTTCCACTGTTCATACAAT +TGAGGCTGGAGTCCCCCAAGGCAGCGTTCTTGGGCCAACCTTATACCTCATCTATACAGC +CGACATCCCTACAAATAGTCGCTTAACGGTATCCACATTTGCCGACGATACAGCTATCCT +TAGCCGTTCAAGGTCCCCTATCCAAGCTACAGCACAGTTGGCACTGTACCTCATCGACAT +TGAGAAGTGGCTCTCTGACTGGCGAATAAAAGTAAACGAGCAAAAATGCAAGCACGTGAC +GTTTACGCTAAACAGACAAGACTGTCCTCCGCTCTTGTTGAACAGCATACCACTCCCGAA +AGCAGACGAGGTAACGTACCTAGGAGTACACCTAGACAGAAGACTCACATGGCGCAGGCA +CATTGAAGCCAAAAAAACCCAACTTAAACTCAAAGCCAACAACTTACACTGGCTCATCAA +CTCTGGTTCTCCGCTCAGCCTAGATCACAAGGTCTTGCTCTACAATTCTATATTGAAACC +AATCTGGACCTATGGCTCACAGTTATGGGGCAATGCCAGCAACAGCAATATTGACATCAT +TCAGCGAGCACAATCAAAGATTCTGAGAACCATCACTGGGGCACCGTGGTACGTTCGGAG +TGAAAACATCCAAAGAGACTTAAATATCCCATCAGTTACCAACGCAATCACGGAACTTAA +GGAAAAATACCATAGCAAGCTTCACACGCACCCCAACCACCTAGCGCGAGGTCTAATCCA +GCTCAGCAGCCGTTCCCGTCTCCGGCGAAAGGACCTACCAACCCAGCGAATAAATTATTA +GGGCCGTTTAAACATAGAACAGTTGGAAAAATAATACAACTGTTCAAAAAATACTTGTTA +TAGTTAAGATTTTTAAACTTATTGTTAGTTCTTATACAAGAAGATTCAATAAATAAAAGC +AAAGTAAAATAAAAAAAAAAAAAAAAAA |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Jun 13 12:52:17 2019 -0400 +++ b/tool_data_table_conf.xml.sample Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -5,4 +5,9 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/bwa_mem_index.loc" /> </table> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> </tables> |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be update_mapq.xml --- a/update_mapq.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/update_mapq.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.1"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.2"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5eb0ec276ea5 -r 7191da0bc7be write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Thu Jun 13 12:52:17 2019 -0400 +++ b/write_supplementary_fastq.xml Sun Jul 28 12:59:08 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.1"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.2"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.1">readtagger</requirement> + <requirement type="package" version="0.5.2">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |