| Previous changeset 2:8d31d5da8662 (2025-07-19) Next changeset 4:0a4456785b0a (2025-08-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong commit 5261d1ca6aeb4f7d84769372b1fdad1db59e08b5 |
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modified:
fastplong.xml |
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added:
test-data/quality_cutting_output.fastq |
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| diff -r 8d31d5da8662 -r 23f75f8716cf fastplong.xml --- a/fastplong.xml Sat Jul 19 08:24:14 2025 +0000 +++ b/fastplong.xml Fri Aug 15 14:07:06 2025 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT"> +<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT"> <description>Filter and trim long reads</description> <creator> <organization name="Masaryk University" url="https://www.muni.cz/"/> @@ -6,7 +6,7 @@ </creator> <macros> <token name="@TOOL_VERSION@">0.3.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">fastplong</requirement> @@ -155,12 +155,6 @@ --cut_front --cut_tail - #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_window_size): - --cut_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_window_size - #end if - #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_mean_quality): - --cut_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_mean_quality - #end if #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size): --cut_front_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size #end if @@ -301,20 +295,18 @@ </param> <when value="none"/> <when value="both"> - <param argument="--cut_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/> - <param argument="--cut_mean_quality" type="integer" optional="true" min="1" max="60" value="20" label="Mean quality threshold" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is 20 (== Q20)."/> - <param argument="--cut_front_window_size" type="integer" optional="true" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/> - <param argument="--cut_front_mean_quality" type="integer" optional="true" min="1" max="60" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/> - <param argument="--cut_tail_window_size" type="integer" optional="true" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/> - <param argument="--cut_tail_mean_quality" type="integer" optional="true" min="1" max="60" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/> + <param argument="--cut_front_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/> + <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/> + <param argument="--cut_tail_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/> + <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/> </when> <when value="front"> <param argument="--cut_front_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/> - <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="60" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/> + <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/> </when> <when value="tail"> <param argument="--cut_tail_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/> - <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="60" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/> + <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/> </when> </conditional> </section> @@ -350,16 +342,30 @@ </assert_contents> </output> </test> + <test expect_num_outputs="3"> <param name="in" value="input.fastq"/> + <section name="read_mod_options"> + <section name="cutting_by_quality_options"> + <conditional name="qual_trim"> + <param name="trim_side" value="both"/> + </conditional> + </section> + </section> <section name="output_options"> <param name="report_json" value="true"/> </section> - <output name="out" file="output.fastq"/> + <output name="out" file="quality_cutting_output.fastq"/> <output name="report_json"> <assert_contents> <has_text text='summary": {'/> <has_text text='fastplong_version": "@TOOL_VERSION@'/> + <has_text text="--cut_front"/> + <has_text text="--cut_tail"/> + <has_text text="--cut_front_window_size 4"/> + <has_text text="--cut_front_mean_quality 20"/> + <has_text text="--cut_tail_window_size 4"/> + <has_text text="--cut_tail_mean_quality 20"/> </assert_contents> </output> </test> |
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| diff -r 8d31d5da8662 -r 23f75f8716cf test-data/quality_cutting_output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quality_cutting_output.fastq Fri Aug 15 14:07:06 2025 +0000 |
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| @@ -0,0 +1,16 @@ +@name +GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name2 +GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name3 +GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name4 +GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE |