Mercurial > repos > iuc > filtlong

annotate filtlong.xml @ 3:e6d48d485920 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
author iuc
date Thu, 24 Feb 2022 21:21:47 +0000
parents 924cf0c5b51e
children 428fd2cee5d9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
1 <tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
2 <description>Filtering long reads by quality</description>
2
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
3 <macros>
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
5 </macros>
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
7 <version_command>filtlong --version</version_command>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
9 filtlong
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
10 #if $output_thresholds.target_bases:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
11 --target_bases '$output_thresholds.target_bases'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
12 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
13 #if $output_thresholds.keep_percent:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
14 --keep_percent '$output_thresholds.keep_percent'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
15 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
16 #if $output_thresholds.min_length:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
17 --min_length '$output_thresholds.min_length'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
18 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
19 #if $output_thresholds.min_mean_q:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
20 --min_mean_q '$output_thresholds.min_mean_q'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
21 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
22 #if $output_thresholds.min_window_q:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
23 --min_window_q '$output_thresholds.min_window_q'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
24 #end if
3
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
25 #if $output_thresholds.max_length:
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
26 --max_length '$output_thresholds.max_length'
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
27 #end if
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
28 #if $external_references.assembly:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
29 --assembly '$external_references.assembly'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
30 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
31 #if $external_references.illumina_1:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
32 --illumina_1 '$external_references.illumina_1'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
33 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
34 #if $external_references.illumina_2:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
35 --illumina_2 '$external_references.illumina_2'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
36 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
37 --length_weight '$score_weights.length_weight'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
38 --mean_q_weight '$score_weights.mean_q_weight'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
39 --window_q_weight '$score_weights.window_q_weight'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
40 $read_manipulation.trim
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
41 #if $read_manipulation.split:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
42 --split '$read_manipulation.split'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
43 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
44 #if $other.window_size:
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
45 --window_size '$other.window_size'
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
46 #end if
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
47 '$input_file' > output.fastq
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
48 ]]></command>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
49 <inputs>
2
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
50 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
51 <section name="output_thresholds" title="Output thresholds">
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
52 <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"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
53 <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)"/>
3
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
54 <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
55 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
56 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
57 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
58 </section>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
59 <section name="external_references" title="External references">
2
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
60 <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
1
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
61 <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
62 <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
63 </section>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
64 <section name="score_weights" title="Score weights">
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
65 <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
66 <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
67 <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
68 </section>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
69 <section name="read_manipulation" title="Read manipulation">
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
70 <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
71 <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
72 </section>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
73 <section name="other" title="Other">
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
74 <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
75 </section>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
76 </inputs>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
77 <outputs>
1
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
78 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
79 </outputs>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
80 <tests>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
81 <test>
2
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
82 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
83 <param name="min_length" value="1000"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
84 <param name="keep_percent" value="50"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
85 <param name="target_bases" value="500000000"/>
1
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
86 <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
87 </test>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
88 <test>
2
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
89 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
924cf0c5b51e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
iuc
parents: 1
diff changeset
90 <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
1
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
91 <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
92 <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
93 <param name="min_length" value="1000"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
94 <param name="keep_percent" value="90"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
95 <param name="target_bases" value="500000000"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
96 <param name="trim" value="True"/>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
97 <param name="split" value="500"/>
1
33efcf418297 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
iuc
parents: 0
diff changeset
98 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
99 </test>
3
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
100 <test>
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
101 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
102 <param name="max_length" value="5000"/>
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
103 <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
e6d48d485920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
iuc
parents: 2
diff changeset
104 </test>
0
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
105 </tests>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
106 <help><![CDATA[
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
107 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.
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
108 ]]></help>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
109 <citations>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
110 <citation type="bibtex">
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
111 @misc{rrwick2017,
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
112 author = {Wick, Ryan},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
113 year = {2017},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
114 title = {Filtlong},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
115 publisher = {GitHub},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
116 journal = {GitHub repository},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
117 url = {https://github.com/rrwick/Filtlong},
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
118 }
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
119 </citation>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
120 </citations>
f7c6dcf60964 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a
iuc
parents:
diff changeset
121 </tool>