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comparison pbccs.xml @ 0:f159c3da2ffc draft default tip

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
author galaxy-australia
date Fri, 18 Mar 2022 02:10:52 +0000
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-1:000000000000 0:f159c3da2ffc
1 <tool id="pbccs" name="CCS" version="0.1.0" python_template_version="3.5">
2 <description>Generate accurate consensus sequences from subreads</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"> <![CDATA[
9 mkdir -p ./tmp &&
10 cp '$input_file' ./tmp/input.bam &&
11 cd ./tmp/ &&
12 ccs
13 -j 4
14 #if $input_filter_options.minLength:
15 --minLength '$input_filter_options.minLength'
16 #end if
17 #if $input_filter_options.maxLength:
18 --maxLength '$input_filter_options.maxLength'
19 #end if
20 #if $input_filter_options.minPasses:
21 --minPasses '$input_filter_options.minPasses'
22 #end if
23 #if $input_filter_options.minIdentity:
24 --minIdentity '$input_filter_options.minIdentity'
25 #end if
26 #if $input_filter_options.zmws:
27 --zmws '$input_filter_options.zmws'
28 #end if
29 #if $model_override_options.modelPath:
30 --modelPath '$model_override_options.modelPath'
31 #end if
32 #if $model_override_options.modelSpec:
33 --modelSpec '$model_override_options.modelSpec'
34 #end if
35 #if $output_filter_options.minPredictedAccuracy:
36 --minPredictedAccuracy '$output_filter_options.minPredictedAccuracy'
37 #end if
38 #if $output_filter_options.minReadScore:
39 --minReadScore '$output_filter_options.minReadScore'
40 #end if
41 #if $output_filter_options.maxDropFraction:
42 --maxDropFraction '$output_filter_options.maxDropFraction'
43 #end if
44 #if $processing_options.byStrand:
45 --byStrand '$processing_options.byStrand'
46 #end if
47 #if $processing_options.noPolish:
48 --noPolish '$processing_options.noPolish'
49 #end if
50 #if $processing_options.richQVs:
51 --richQVs '$processing_options.richQVs'
52 #end if
53 #if $if_log.log_options == "yes":
54 --logFile '$log_output'
55 --logLevel '$if_log.loglevel'
56 #end if
57 #if $output_options.reportFile:
58 --reportFile ccs_report.txt
59 #end if
60 input.bam
61 output.bam
62 && mv output.bam '$bam_output'
63 && mv ccs_report.txt '$report_output'
64 2>&1
65
66 ]]></command>
67 <inputs>
68 <param name="input_file" type="data" format="bam" label="Input Subreads" help="Subreads (subreads.bam)"/>
69 <section name="input_filter_options" title="Input Filter Options" expanded="False">
70 <param argument="--minLength" type="integer" value="10" label="Minimum length" help="Minimum draft length before polishing. [10]" />
71 <param argument="--maxLength" type="integer" value="21000" label="Maximum length" help="Maximum draft length before polishing. [21000]"/>
72 <param argument="--minPasses" type="integer" value="3" label="Minimum number of subreads" help="Minimum number of subreads required to generate CCS. [3]" />
73 <param argument="--minIdentity" type="float" value="0.82" label="top N passes" help="Minimum identity of a subread aligned to the draft consensus to use it for polishing. 0 disables this filter. [0.82]" />
74 <param argument="--minSnr" type="float" value="2.5" label="Minimum SNR of subreads" help="Minimum SNR of subreads to use for generating CCS [2.5]"/>
75 <param argument="--zmws" type="text" value="all" label="Generate CCS for the provided comma-separated hole number ranges only." help="Default=all" />
76 </section>
77 <section name="model_override_options" title="Model Override Options" expanded="False">
78 <param argument="--modelPath" type="data" format="txt" optional="True" label="Model File" help="a model file or directory containing model files." />
79 <param argument="--modelSpec" type="text" value="" optional="True" label="Chemistry" help="Name of chemistry or model to use, overriding default selection."/>
80 </section>
81 <section name="processing_options" title="Processing Options" expanded="False">
82 <param argument="--byStrand" type="boolean" truevalue="--byStrand" falsevalue="" checked="false" label="Generate a consensus for each strand." />
83 <param argument="--noPolish" type="boolean" truevalue="--noPolish" falsevalue="" checked="false" label="Only output the initial template derived from the POA (faster, less accurate)." />
84 <param argument="--richQVs" type="boolean" truevalue="--richQVs" falsevalue="" checked="false" label="Emit dq, iq, and sq rich quality tracks." />
85 </section>
86 <section name="output_filter_options" title="Output Flter Options" expanded="False">
87 <param argument="--minPredictedAccuracy" type="float" value="0.9" label="Mininum predicted accurary" help="i.e 0.9"/>
88 <param argument="--minReadScore" type="float" value="0.75" label="Minimum read score of input subreads" help="i.e 0.75"/>
89 <param argument="--maxDropFraction" type="float" value="0.34" label="Maximum fraction of subreads dropped by polishing (not input filters) before skipping ZMW." help="i.e 0.34" />
90 </section>
91 <section name="output_options" title="Output Files Options" expanded="False">
92 <param argument="--reportFile" type="boolean" truevalue="True" falsevalue="False" checked="False" label="write the results report."/>
93 </section>
94 <conditional name="if_log">
95 <param type="select" name="log_options" label="show log option">
96 <option value="yes">Yes</option>
97 <option value="no" selected="true">No</option>
98 </param>
99 <when value="yes">
100 <param argument="--logLevel" name="loglevel" type="select" label="Log Level">
101 <option selected="True" value="WARN">WARN</option>
102 <option value="TRACE">TRACE</option>
103 <option value="DEBUG">DEBUG</option>
104 <option value="INFO">INFO</option>
105 <option value="FATAL">FATAL</option>
106 </param>
107 </when>
108 <when value="no">
109 </when>
110 </conditional>
111 </inputs>
112 <outputs>
113 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: CCS reads in BAM format"/>
114 <data format="txt" name="report_output" label="${tool.name} on ${on_string}: CCS reads report"/>
115 <data format="txt" name="log_output" label="${tool.name} on ${on_string}: log" >
116 <filter>if_log['log_options'] == 'yes' </filter>
117 </data>
118 </outputs>
119 <tests>
120 <test><!-- test with default settings -->
121 <param name="input_file" ftype="bam" value="input.subreads.bam"/>
122 <output name="bam_output" ftype="bam" file="output.bam" />
123 <output name="log_output" ftype="txt" file="log.txt" />
124 <output name="report_output" ftype="txt" file="report.txt" />
125 </test>
126 </tests>
127 <help><![CDATA[
128 @PBCCS_OVERVIEW@
129
130 For detailed information on psp-gen, click here_, or view the license_.
131
132 .. _here: https://github.com/nlhepler/pbccs
133 .. _license: https://github.com/nlhepler/pbccs/blob/master/LICENSE
134
135 **Command Documentation**
136
137 CCS will generate consensus sequence.
138
139
140 ]]></help>
141 <expand macro="citations"/>
142 </tool>
143