Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison cfsan_bettercallsal.xml @ 2:4678c2cd1c9e

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"planemo upload"
author kkonganti
date Tue, 06 Jun 2023 09:46:25 -0400
parents 365849f031fd
children e06ae620fcb2
comparison
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1:365849f031fd 2:4678c2cd1c9e
34 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 34 ln -sf '$pair.forward' './cpipes-input/$read_R1';
35 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 35 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
36 #end for 36 #end for
37 #end if 37 #end if
38 $__tool_directory__/0.5.0/cpipes 38 $__tool_directory__/0.5.0/cpipes
39 --pipeline $input_read_type_cond.pipeline_cond.pipeline 39 --pipeline bettercallsal
40 --input \${pwd_path}/cpipes-input 40 --input \${pwd_path}/cpipes-input
41 --output \${pwd_path}/cpipes-output 41 --output \${pwd_path}/cpipes-output
42 --fq_suffix '${input_read_type_cond.fq_suffix}' 42 --fq_suffix '${input_read_type_cond.fq_suffix}'
43 #if (str($input_read_type_cond.input_read_type) == "single_long"): 43 #if (str($input_read_type_cond.input_read_type) == "single_long"):
44 --fq_single_end true 44 --fq_single_end true
51 #end if 51 #end if
52 --bcs_thresholds $bcs_thresholds 52 --bcs_thresholds $bcs_thresholds
53 --fq_filename_delim '${fq_filename_delim}' 53 --fq_filename_delim '${fq_filename_delim}'
54 --fq_filename_delim_idx $fq_filename_delim_idx 54 --fq_filename_delim_idx $fq_filename_delim_idx
55 -profile kondagac; 55 -profile kondagac;
56 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 56 mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
57 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1; 57 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1;
58 rm -rf ./work > /dev/null 2>&1 || exit 1 58 rm -rf ./work > /dev/null 2>&1 || exit 1
59 ]]></command> 59 ]]></command>
60 <inputs> 60 <inputs>
61 <conditional name="input_read_type_cond"> 61 <conditional name="input_read_type_cond">
72 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" /> 72 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
73 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/> 73 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/>
74 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/> 74 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
75 </when> 75 </when>
76 </conditional> 76 </conditional>
77 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step." 77 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step"
78 help="The default value of 10 is suitable for almost all scenarios."/> 78 help="The default value of 10 is suitable for almost all scenarios."/>
79 <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal." 79 <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal"
80 help="The default value sets strictest thresholds that tends to filter out most of the false positive hits."> 80 help="The default value sets strictest thresholds that tends to filter out most of the false positive hits.">
81 <option value="strict" selected="true">strict</option> 81 <option value="strict" selected="true">strict</option>
82 <option value="relax">relax</option> 82 <option value="relax">relax</option>
83 </param> 83 </param>
84 <conditional name="sourmash_cond"> 84 <conditional name="sourmash_cond">
85 <param name="run" type="select" label="Run sourmash" 85 <param name="run" type="select" label="Run sourmash"
86 help="Should sourmash be used for additional genome fraction filtering."> 86 help="Should sourmash be used for additional genome fraction filtering">
87 <option value="true" selected="true">yes</option> 87 <option value="true" selected="true">yes</option>
88 <option value="false">no</option> 88 <option value="false">no</option>
89 </param> 89 </param>
90 <when value="true"> 90 <when value="true">
91 <param name="sfhpy_fcv" type="text" value="0.1" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing." 91 <param name="sfhpy_fcv" type="text" value="0.1" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
92 help="The default value is set at 10% coverage threshold."/> 92 help="The default value is set at 10% coverage threshold."/>
93 </when> 93 </when>
94 <when value="false"> 94 <when value="false">
95 <param name="sfhpy_fcv" type="select" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing." 95 <param name="sfhpy_fcv" type="select" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
96 help="THIS OPTION IS IGNORED IF SOURMASH TOOL IgreS DISABLED."> 96 help="THIS OPTION IS IGNORED IF SOURMASH TOOL IgreS DISABLED.">
97 <option value="NA" selected="true">N/A</option> 97 <option value="NA" selected="true">N/A</option>
98 </param> 98 </param>
99 </when> 99 </when>
100 </conditional> 100 </conditional>
105 <option value="kondagac" selected="true">conda</option> 105 <option value="kondagac" selected="true">conda</option>
106 <option value="cingularitygac">singularity</option> 106 <option value="cingularitygac">singularity</option>
107 </param> --> 107 </param> -->
108 </inputs> 108 </inputs>
109 <outputs> 109 <outputs>
110 <data name="multiqc_report" format="html" label="${input_read_type_cond.pipeline_cond.pipeline}: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> 110 <data name="multiqc_report" format="html" label="bettercallsal: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
111 </outputs> 111 </outputs>
112 <tests> 112 <tests>
113 <!--Test 01: long reads--> 113 <!--Test 01: long reads-->
114 <test expect_num_outputs="2"> 114 <test expect_num_outputs="2">
115 <param name="input"> 115 <param name="input">