| Previous changeset 2:a72af9de6bf5 (2021-03-31) Next changeset 4:1f296803dfa3 (2023-11-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb" |
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modified:
filtlong.xml macros.xml |
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added:
test-data/output_max_length.fastq |
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| diff -r a72af9de6bf5 -r 41b2ad601cf0 filtlong.xml --- a/filtlong.xml Wed Mar 31 08:19:02 2021 +0000 +++ b/filtlong.xml Thu Feb 24 21:22:16 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Filtering long reads by quality</description> <macros> <import>macros.xml</import> @@ -22,6 +22,9 @@ #if $output_thresholds.min_window_q: --min_window_q '$output_thresholds.min_window_q' #end if + #if $output_thresholds.max_length: + --max_length '$output_thresholds.max_length' + #end if #if $external_references.assembly: --assembly '$external_references.assembly' #end if @@ -48,6 +51,7 @@ <section name="output_thresholds" title="Output thresholds"> <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> + <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/> <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/> <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/> <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> @@ -93,6 +97,11 @@ <param name="split" value="500"/> <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/> </test> + <test> + <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> + <param name="max_length" value="5000"/> + <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/> + </test> </tests> <help><![CDATA[ Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. |
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| diff -r a72af9de6bf5 -r 41b2ad601cf0 macros.xml --- a/macros.xml Wed Mar 31 08:19:02 2021 +0000 +++ b/macros.xml Thu Feb 24 21:22:16 2022 +0000 |
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| @@ -1,9 +1,10 @@ <macros> - <token name="@WRAPPER_VERSION@">0.2.0</token> + <token name="@TOOL_VERSION@">0.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">filtlong</requirement> + <requirement type="package" version="@TOOL_VERSION@">filtlong</requirement> </requirements> </xml> </macros> |
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| diff -r a72af9de6bf5 -r 41b2ad601cf0 test-data/output_max_length.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_max_length.fastq Thu Feb 24 21:22:16 2022 +0000 |
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| b'@@ -0,0 +1,12 @@\n+@test_sort_1\n+AGCGGGACTCTTCCCGAGGGGCCTGGAAATACCACGGATTCCAATAGTACGTTCTGTTAGCTGGGTGTCTTTATGCATGCCAAGGTTCGAACCTCCGGCCATGTTGGATGTTGAAAAGGTAGCCAGCGAGATGGAAGAAGGCCAAGGCTTCATATTACCCCGAATTCTCAAGGTGGATAAGGGGAACTAACGGCTGCGAGCATGCAGCTGGCATCAATGGCCAGGCGACAGATTTACTCTACTTTCCGCTGCTTGTTCTGGATTGGGATGTTAACCCTTTGATCCCACAGAGGTCAGCGGAGAAAACAACGTCTAAATATAGTCGGACAGACTGTAGCGACCCGGTTAGCACTCCCTAATTTTATCTAACTAGGCGGACACACTCTTACCACAGGGGCTCCAAGGTTCTCTCATTTCCGTGGGTGTAGCAACGTCCTATTCTTATGCGGACGCGAAGTAACGAGTATTCTCTTGGATTTTAACTGAGCTATCACTCCGCGTGAAGGATAACCGGCTTGACTAAAGGAGACGGTCAGTCGCAGAGGGCAACGCGCTATATACATTCGGTTTATTGAGTTCACCCTGGATAGTGACGCGGCCCTGGTTGTAGGTCGGGGCAAACTCTGAAATTGCTACTCGTATACAGGGTTGTGCGCTCGTAAGGACTCCCCCCTGGCGTCGAAGCTAGTTCGACAAAATGGCCCCGGAAGACGTTATCTAGATGAGTCTGGGTGGCTTTCAAGAATTCGCCTATCTTGGTACCTGGCCCTAACGATCAGACAGGCGCACTGCTGATGAGGGCATGTACCGACCATACGGTTTTTCTTCAGGCAAATGCCCGTTCCGGTGTCCGTGGTCAAGACTCAAAATCTCCCCTAAGGCTGTCACGAATTAGAGTTTCGTGTGAGAGATTAGTGTTAGCCCTCAGTGGGTCCTAATAAGAACCCACTAAGTTAGCCTCGCCGGTACGCAGACCTAGAGACTTGTTGGTGGGCAGCTTCTGCGCTGTTGGCATTCCTGCATAAAGAGAAACGTTATCGGCTGCCGGTGTCATCTGCCAGTGCTGCCGAGTCGAGCTTGTAGCACTCATTGAAGGTGCTGTGAGCTGCACGCCTCCACTAATTTAATCCCCGTCGCAAAGTTGGTCAGACCAGGAGCCTTCAGTGCACTGTGACAACTGGAATTCCGACTCCGGAAAAGTGCAATGGGTGTCCAGTGGACGACTTCTTGTGATTCGCGCCCGCGCCGCGTCCACAGGGGGACTCGGCGAAAAGTACAAAAGTAGGGGGAGCGCCCTGAGGAGAGTGGATCGTGCCGTCACCGGGTGACGGGTACAAGAACCTACTACTAGTGACGATGCTCTTAGATGGAGTGTAGCACGATCTTCACGGATAAAATAATGAAACAAACTGGGGCCGTTGGGCCCCCGAAGTATATGAACTGCGGCCATGTATGTTATGAATCCCCTCGGGTTCGAGGCTGCTCAAAAGTCTGCGTAGGACTCTCATCGGGACCTATACTAGATGGCGATGCGGAATACAGCGGCCTAGCTTTTATGCGATGTGCGGGGATAATTCTAATAGTTGCGGCTGGTCCATAACCGTGGACGTCGTATATTGGCAGACCTGCACAGTTGGTCCGATTAGACATACAGCACCCTTCTACATCCTGTTGTTCTGGAGAAGCCCACTCTAGTAGGACGGTTTACCTATGGACATGCGGTGTCCTAAATCATCCTACCGGAATTCTCATGCACTTCTGCCGTTCCCCCGAACATTCTAGTGGTGGGCTCGGGCTGCTGATAATCCACTCCATTGGGTGATACAAGAGGCGAGTTTGCCTTAGTTTGGGCAGGTCATGAAACCAAGCAACCGCATGCTTAGCTGGCTAATTGTTCGACTCGGCCACCAGCAAACTGTCGAAACGCGTAGAAAGTACAATTCCGTAAGCGAGTTCGGAATCCAGACCCGCGGCAATGCCCTCTCTTCCTACGCAGCGACCCCCTGTTTACACAGACAAGGCCCCGATGGCCAATCGGGAGTCTCGACGAGTGCCATAGAGGCGCCCTACCGGCGTCAGTGGGGGTGATTAATCACTTCACTGGTTCGCGGTGGGCTACGCGCTCACCTAGCTTCCCCGTAGTGTATTGACGAGTGTGGGCCCAGGATATGGAAGTTAAGGCTGGAGGAATAGATAACCGTCGTACCTCCCCTGGACGAGATAGCACTAAATCCTGGAAATGAGACGGATCCGAGAGTTCTGATAATGTTCGAGATGGGACAACAGGCGAATCTCGCAAACGTGCTTCAAAATATAACGTAGCATCCCGCTTATGGGCTTTATCGCGAAACCTGACAGCGCTCCCTCAAACCCCTAGTTCGGAAAATCGTGTCGCTCCTACAGTCCATCACTCAACTTCAGTTGAGCAATAAGTTTAGGGCGCGTCACTCTATCTACTTTACTGCTGAATGGACCCTTGTGTGGATCGTAAACCTTCAAGTCCCTGGGACTGCCTGTTCTTGCGATGATAAGATTAAGTGTTTGCCCGTTTGCCAACCATCCCTCAAATCTCGTTGATGAACCTGCCCCTTCTGTTCCATTACCAATCGACGGCTCTAACTTTTCAATCTGTGGCATGGACCCCATAAAGAGGGACCAGCGTTCAGGGAGACTTCTACAAACTTACGTTACATTATACCGTTCGCGGTGAGCGTGCGGTCAAGCATTCCAAAAGTACTCCGCGAGCCGTACGATCGACCTCTAGTATACTCCTGGTGCGGAGCAAACGATTTGAGCAGGCCTCATATAGAATGTGCAATCGCTCATTGTCGCAAAGCCACAACCAGTCACGCCGTTCGTCGACTACCACCCACTTCGTGGATGTGCGCCAAGTCTGTCTCCAGCTCTCAAGACTCATTGCAACTTGCCAATAACCTCAGTGCCTTGTCACTTCGAGTTCTTGAGGAATAGTCAGGGTCCTTAAACTTCATCGACTCGGCACAGTCTCTAGCCTCATTACTTCCCATTCCGGCCCGATGTGGAAGCGGTCCGGCTACTCAAATGCTCCCGGAGACCGAAGATTTCGGGACCTTTCGTTGTCAGACGCCAGTCATTGTTGCCTCTAACTGCATTGGAATCTGGCCCAAATAGAGATTGACCTCGGGAATCCGTCGCTGGGCAGGGCGTCGTACTCTGAACGGGACATCACTCCCGACCACCGGGGGGCGTCGTAGGTGCAGCAGACTGACAAATCCGTCCCAGTCGACTTATGTTCGCATGTCGTTATTAACTGCCTTGTACCTACGGTATGTACTGAACCACCGAGATCAGGGCAGGTTGAGCAAATTCATATCTCAAGGTGTGTCGAGAAAAAACGATTTAAGCTCTAGACCGGGAGTGCTGGTCAGAGTGTTCTGCTCACAAGGAAGCAATTCGGTGTTGGGTACCAATCAGAAATCACACCGTGGCTCTGAGCTTAATCCCTTGGGTTGGGCAACCGGGAGGACCAAGAGTACCGGCGACGGCCTCTGATTCTTGACGGTATAGGAGACATGCCTATACACGTTCGAGAGTAGTGACAGCATAGGATGCCTCAACGCTTTTACTCACGAGTGTGTGGTCCAATCTTGATGTCTAGACATGAGTTTTTCTAACGAGTGAACGGTATCCTATCCGCCCTCTGGATCAGCGGTTTCGGGGGTCCCTATGATGCTGTTCATATGCTCTGTCCATTGATTTGAGCCTACGGTATGAAGCACTCGCGGTGAAAAGGTTGCTGTAACCCGCGGGTGGTTACGATCTAATCTTCTGGTACGAAGGCGTGCCGTTACGCCAAAACTGGTACCTTGGTGTTTTTGCTGATCTCCAGAATTTTTGCTGTACTATTCCAATTTAGGAGTCATGAGTCCGGAATGTCATTCCGACAAGCAGTATTCCCAACAGAGAACACTTGCATACTCGTTAATGA'..b'//1//00/00//00/01111/10/01/0//0/////11100/10/11/0001100//1//1/011101100/0/01110///00/0/0/1///10//10/010//0000///01/00/1/1/01///11/100/11110/111011///0101/1/000/11/00/0/1011/10/100/10111/001//101//1/1111011/11/1//1011100//0000/011100//110001/0/010/01101010000//11/1//0//1/110/1/0/1/0/0100/1//1//11/01//010//1/01//01//10110//01011//0/0///0///1001/11//01/011/01001/110//00/0/0/01/010/0//01101/010/00/00001/10////0//01111//0//000/0//110//00110//1//1000010100/0/1//0//101/1010100101/10/01000100/01000101/01///11/01//00010///00101/1010/0/000/00////1/001110/00/0010/10011/1//010/0011/011/00/011/0111/0/00//000///0100/1100101001/1//111/1/1/0///1/11/0/1/0/00//1110/0101///01/1/1////////101000/1/00/0//00/100//100/0/000///101/0//1/101/00011011000//1//1/11/10100//0/0/01000110101/00/1110/1010/111110000/1/0/1/00//1100/11/00/10/1000/00/01/00/01001111/1////1/0/1//0101/1/0011010110//1/0/0/110/1//00/11000/1/1/1//0010/011/0///10/0/0/011//10/10///0100000000//01100/00/00/0111//01//00/0110110/110/100010/1/1/1001/10///0//00/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