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comparison SsuisSerotyping_pipeline.xml @ 0:135510a99b5a draft

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author p.lucas
date Thu, 09 May 2019 04:14:19 -0400
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1 <tool id="SsuisSerotyping_pipeline" name="Use SsuisSerotyping_pipeline." version="0.1.1">
2 <requirements>
3 <requirement type="package">perl-bioperl</requirement>
4 <requirement type="package">scipy</requirement>
5 <requirement type="package" version="2.7">python</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command><![CDATA[
11 python $__tool_directory__/Prepare_Ssuis_serotypingPipeline.py
12 --fastq_file $input1
13 --scoreName '$output1'
14 --output2 '$output2'
15 --output3 '$output3'
16 --output4 '$output4'
17 --output5 '$output5'
18 --output6 '$output6'
19 --output7 '$output7'
20 --output8 '$output8'
21 #if $optionalfiles.analysis_selector == "specific":
22 --serotype_db '$options.serotype_db'
23 --serotype_definitions '$options.serotype_definitions'
24 --cps2K '$options.cps2K'
25 --Virulence_db '$options.Virulence_db'
26 --recN_db '$options.recN_db'
27 --MLST_definitions '$options.MLST_definitions'
28 --MLST_db '$options.MLST_db'
29 #end if
30 #if $typeofdata.pors == "paired":
31 --ends pe
32 --forward '$typeofdata.forward'
33 --reverse '$typeofdata.reverse'
34 #else:
35 --ends se
36 #end if
37
38 ]]></command>
39 <inputs>
40 <param type="data" name="input1" format="fastq" />
41 <conditional name="optionalfiles">
42 <param name="analysis_selector" type="select" label="Use specific or default configuration?">
43 <option value="default" selected="True">Use default configuration.</option>
44 <option value="specific">Use specific file</option>
45 </param>
46 <when value="default" />
47 <when value="specific">
48 <param type="data" name="serotype_db" format="fasta" label="Serotype database in fasta format." />
49 <param type="data" name="serotype_definitions" format="txt" label="Definition of the serotype database" />
50 <param type="data" name="cps2K" format="fasta" label="Multifasta with cpsH confirmation database" />
51 <param type="data" name="Virulence_db" format="fasta" label="Virulence genes" />
52 <param type="data" name="recN_db" format="fasta" label="recN species specfic gene" />
53 <param type="data" name="MLST_definitions" format="txt" label="Definitions of MLST database file" />
54 <param type="data" name="MLST_db" format="fasta" label="MLST database" />
55 </when>
56 </conditional>
57 <conditional name="typeofdata">
58 <param name="pors" type="select" label="Read option">
59 <option value="single" selected="True">Single-end</option>
60 <option value="paired">Paired-end</option>
61 </param>
62 <when value="single" />
63 <when value="paired">
64 <param type="text" name="reverse" value="_R1" />
65 <param type="text" name="forward" value="_R2" />
66 </when>
67 </conditional>
68 </inputs>
69 <outputs>
70 <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" />
71 <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" />
72 <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" />
73 <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" />
74 <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" />
75 <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" />
76 <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
77 <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" />
78 </outputs>
79 <tests>
80 <test>
81 <param name="input1" value="/home/plucas/TEST/SsuisSerotyping_pipeline/input_fastq/SS1218_IonXpress_008_R_2016_02_23.soft_clean.trimmomatic_trimmed.fastq"/>
82 <output name="output1" file="/home/plucas/TEST/SsuisSerotyping_pipeline/results/Results_FinalResults.txt"/>
83 </test>
84 </tests>
85 <help><![CDATA[
86 Implementation of the S. suis serotyping pipeline:
87
88 perl Ssuis_serotypingPipeline.pl --fastq_directory /path/to/fastq/directory --scoreName Scores_output_name --serotype_db serotype.fasta --serotype_definitions serotype_definitions.txt --cps2K cps2K.fasta
89
90 --fastq_directory Path to directory containing paired-end fastq files.
91 Must be full path to directory, please do not use '.'
92 or '..' to declare path
93 If no path is given, the current working
94 directory is used
95 --scoreName Name of SRST2 results file
96 [optional: default name 'Results']
97 --serotype_db Multifasta file containing the serotype database
98 (Ssuis_Serotyping.fasta)
99 [If none is provided, Ssuis_Serotyping.fasta is looked
100 for in the directory containing the script]
101 --serotype_definitions Text file containing the definitions for the
102 serotype database file
103 (Ssuis_Serotyping_Definitions.txt)
104 [If none is provided, Ssuis_Serotyping_Definitions.txt is looked
105 for in the directory containing the script]
106 --cps2K Multifasta file containing the cpsH confirmation database
107 (Ssuis_cps2K.fasta)
108 [If none is provided, Ssuis_cps2K.fasta is looked
109 for in the directory containing the script]
110 --MLST_db Multifasta file containing the MLST database
111 (Streptococcus_suis.fasta)
112 [If none is provided, Streptococcus_suis.fasta is looked
113 for in the directory containing the script]
114 --MLST_definitions Text file containing the definitions for the
115 MLST database file
116 (ssuis.txt)
117 [If none is provided, ssuis.txt is looked
118 for in the directory containing the script]
119 --recN_db Fasta file containing the recN species specfic gene
120 (recN_Full.fasta)
121 [If none is provided, recN_full.fasta is looked
122 for in the directory containing the script]
123 --Virulence_db Multifasta file containing the Virulence genes
124 (Virulence.fasta)
125 [If none is provided, Virulence.fasta is looked
126 for in the directory containing the script]
127 --forward Indicator delimiting the forward reads file for
128 paired read fastq files
129
130 This option is ignored if single-end reads is selected
131 [optional: default '_R1']
132
133 --reverse Indicator delimiting the reverse reads file for
134 paired read fastq files
135
136 This option is ignored if single-end reads is selected
137 [optional: default '_R2']
138
139 --ends Indicates whether the reads are paired-end (pe) or single-end (se)
140 [optional: default 'pe']
141
142 Note: We recommend using paired end reads of at least 100nt in length
143 and at least 30X coverage.
144 We have not tested the efficiency of the pipeline with reads shorter than 80nt.
145 ]]></help>
146 <citations>
147 <citation type="bibtex">
148 @misc{githubSsuisSerotyping_pipeline,
149 author = {LastTODO, FirstTODO},
150 year = {TODO},
151 title = {SsuisSerotyping_pipeline},
152 publisher = {GitHub},
153 journal = {GitHub repository},
154 url = {https://github.com/streplab/SsuisSerotyping_pipeline},
155 }</citation>
156 </citations>
157 </tool>