| Previous changeset 8:bf8ffb337cbe (2017-03-05) Next changeset 10:c179d081b6ba (2017-03-09) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml |
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added:
test-data/remapped_supplementary.bam test-data/supplementary.bam test-data/supplementary.fastq test-data/supplementary_new_mapq.bam update_mapq.xml write_supplementary_fastq.xml |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 add_matesequence.xml --- a/add_matesequence.xml Sun Mar 05 13:29:42 2017 -0500 +++ b/add_matesequence.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.4"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.5"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.4">readtagger</requirement> + <requirement type="package" version="0.3.5">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 allow_dovetailing.xml --- a/allow_dovetailing.xml Sun Mar 05 13:29:42 2017 -0500 +++ b/allow_dovetailing.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.4"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.5"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.4">readtagger</requirement> + <requirement type="package" version="0.3.5">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 bam_readtagger.xml --- a/bam_readtagger.xml Sun Mar 05 13:29:42 2017 -0500 +++ b/bam_readtagger.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.4"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.5"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.4">readtagger</requirement> + <requirement type="package" version="0.3.5">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 findcluster.xml --- a/findcluster.xml Sun Mar 05 13:29:42 2017 -0500 +++ b/findcluster.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.4"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.5"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.4">readtagger</requirement> + <requirement type="package" version="0.3.5">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/remapped_supplementary.bam |
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| Binary file test-data/remapped_supplementary.bam has changed |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary.bam |
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| Binary file test-data/supplementary.bam has changed |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supplementary.fastq Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -0,0 +1,36 @@ +@HWI-D00405:129:C6KNAANXX:3:2115:7866:72488 +AAAGAAATAATTAGTTTTCCGCTCTTTTTATGTAAAATCGT ++ +BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@HWI-D00405:129:C6KNAANXX:3:2210:21010:12528 +AAGAAATAATTAGTTTTCCGCTCTTTTTATGTAAAATCGT ++ +BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@HWI-D00405:129:C6KNAANXX:3:1312:14525:13985 +AATTAGTTTTCCGCTCTTTTTATGTAAAATCGT ++ +BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@HWI-D00405:129:C6KNAANXX:3:2112:20719:46788 +ATTAGTTTTCCGCTCTTTTTATGTAAAATCGT ++ +BBBBBFFFFBFFFFFFFFFFBFFFFFFFFFFF +@HWI-D00405:129:C6KNAANXX:4:1112:20453:89309 +ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCAT ++ +FFFFFFFFFBFBBFFFFFFFFFBBF/BFFF<FB<</F<F +@HWI-D00405:129:C6KNAANXX:4:2201:13501:43210 +ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTGAT ++ +BFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<BFFFFFBFFFFFFBFBF +@HWI-D00405:129:C6KNAANXX:3:1210:5442:13792 +ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCAT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@HWI-D00405:129:C6KNAANXX:4:1112:20453:89309 +ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTG ++ +FFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB +@HWI-D00405:129:C6KNAANXX:3:1210:5442:13792 +ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTG ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary_new_mapq.bam |
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| Binary file test-data/supplementary_new_mapq.bam has changed |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 update_mapq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update_mapq.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -0,0 +1,45 @@ +<tool id="update_mapq" name="Update MAPQ score" version="0.3.5"> + <description>of supplementary alignments</description> + <requirements> + <requirement type="package" version="0.3.5">readtagger</requirement> + </requirements> + <version_command>update_mapq --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path' + ]]></command> + <inputs> + <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/> + <param argument="--remapped_path" label="Extarct MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/> + </inputs> + <outputs> + <data name="output_path" format="bam"/> + </outputs> + <tests> + <test> + <param name="source_path" value="supplementary.bam" ftype="bam"/> + <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/> + <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/> + </test> + </tests> + <help><![CDATA[ +.. code-block:: + + Usage: update_mapq [OPTIONS] + + Update supplementary read MAPQ score after remapping. + + Options: + --source_path PATH Alignment file where supplementary reads should be + updated with new MAPQ scores [required] + --remapped_path PATH Alignment file that contains reads that have been + remapped and contain an updated MAPQ score [required] + --output_path PATH Write all alignments in original_path to this + location. Supplementary reads will take the MAPQ score + as determined by remapping to the alignment file at + `remapped_path` [required] + --version Show the version and exit. + --help Show this message and exit. + + + ]]></help> +</tool> |
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| diff -r bf8ffb337cbe -r 53b71263e2a2 write_supplementary_fastq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_supplementary_fastq.xml Wed Mar 08 05:14:25 2017 -0500 |
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| @@ -0,0 +1,37 @@ +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.5"> + <description>from SAM/BAM alignment files as FASTQ</description> + <requirements> + <requirement type="package" version="0.3.5">readtagger</requirement> + </requirements> + <version_command>write_supplementary_fastq --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + write_supplementary_fastq --input_path '$input' --output_path '$output' + ]]></command> + <inputs> + <param name="input" argument="--input_path" type="data" format="bam"/> + </inputs> + <outputs> + <data name="output" format="fastqsanger"/> + </outputs> + <tests> + <test> + <param name="input" value="supplementary.bam" ftype="bam"/> + <output name="output" file="supplementary.fastq" ftype="fastqsanger"/> + </test> + </tests> + <help><![CDATA[ +.. code-block:: + + Usage: write_supplementary_fastq [OPTIONS] + + Write all supplementary alignments in `input_path` to an output fastq file + at `output_path`. + + Options: + --input_path PATH Collect supplementary reads in this alignment file. + --output_path PATH Write supplementary reads to this FASTQ file. + --help Show this message and exit. + + + ]]></help> +</tool> |