Mercurial > repos > rliterman > csp2

comparison csp2_screen.xml @ 66:90e29c1ddeca

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Thu, 19 Dec 2024 15:55:32 -0500
parents 16b103443761
children 0e9998148a16
comparison
equal deleted inserted replaced
65:c2a886313008 66:90e29c1ddeca
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 9
10 mkdir ./queries ./references; 10 mkdir ./queries ./references;
11 11
12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 12 #if (str($query_fasta.query_fasta_select) == "none"):
13 #for query in $query_fasta: 13 export QUERY_FASTA_ARG="";
14 ln -sf ${query} ./queries/${query.element_identifier}; 14 #elif (str($query_fasta.query_fasta_select) == "collection"):
15 #for _, $query_assembly in enumerate($query_fasta.coll):
16 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
15 #end for 17 #end for
16 export QUERY_FASTA_ARG="--fasta ./queries"; 18 export QUERY_FASTA_ARG="--fasta ./queries";
17 else 19 #else
18 export QUERY_FASTA_ARG=""; 20 #for _, $query_assembly in enumerate($query_fasta.list):
19 fi; 21 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
20 22 #end for
21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 23 export QUERY_FASTA_ARG="--fasta ./queries";
22 #for query in $query_reads: 24 #end if
23 ln -sf ${query} ./queries/${query.element_identifier}; 25
26 #if (str($ref_fasta.ref_fasta_select) == "none"):
27 export REF_FASTA_ARG="";
28 #elif (str($ref_fasta.ref_fasta_select) == "collection"):
29 #for _, $ref_assembly in enumerate($ref_fasta.coll):
30 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
31 #end for
32 export REF_FASTA_ARG="--fasta ./references";
33 #else
34 #for _, $ref_assembly in enumerate($ref_fasta.list):
35 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
36 #end for
37 export REF_FASTA_ARG="--fasta ./references";
38 #end if
39
40 #if (str($query_reads.query_reads_select) == "none"):
41 export QUERY_READS_ARG="";
42 #elif (str($query_reads.query_reads_select) == "collection"):
43 #for _, $pair in enumerate($query_reads.coll):
44 ln -sf ${pair.forward} ./queries/${pair.forward.name};
45 ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
24 #end for 46 #end for
25 export QUERY_READS_ARG="--reads ./queries"; 47 export QUERY_READS_ARG="--reads ./queries";
26 else 48 #else
27 export QUERY_READS_ARG=""; 49 #for _, $read_file in enumerate($query_reads.list):
28 fi; 50 ln -sf ${read_file} ./queries/${read_file.element_identifier};
29 51 #end for
30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 52 export QUERY_READS_ARG="--reads ./queries";
31 #for ref in $ref_fasta: 53 #end if
32 ln -sf ${ref} ./references/${ref.element_identifier}; 54
33 #end for 55 #if (str($ref_reads.ref_reads_select) == "none"):
34 export REF_FASTA_ARG="--ref_fasta ./references"; 56 export REF_READS_ARG="";
35 else 57 #elif (str($ref_reads.ref_reads_select) == "collection"):
36 export REF_FASTA_ARG=""; 58 #for _, $pair in enumerate($ref_reads.coll):
37 fi; 59 ln -sf ${pair.forward} ./references/${pair.forward.name};
38 60 ln -sf ${pair.reverse} ./references/${pair.reverse.name};
39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
40 #for ref in $ref_reads:
41 ln -sf ${ref} ./references/${ref.element_identifier};
42 #end for 61 #end for
43 export REF_READS_ARG="--ref_reads ./references"; 62 export REF_READS_ARG="--ref_reads ./references";
44 else 63 #else
45 export REF_READS_ARG=""; 64 #for _, $read_file in enumerate($ref_reads.list):
46 fi; 65 ln -sf ${read_file} ./references/${read_file.element_identifier};
66 #end for
67 export REF_READS_ARG="--ref_reads ./references";
68 #end if
47 69
48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 70 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
49 export TRIM_ARG="--trim_name $trim_name"; 71 export TRIM_ARG="--trim_name $trim_name";
50 else 72 else
51 export TRIM_ARG=""; 73 export TRIM_ARG="";
60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 && 82 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
61 ls -la CSP2_Screen_Output; 83 ls -la CSP2_Screen_Output;
62 ]]> 84 ]]>
63 </command> 85 </command>
64 <inputs> 86 <inputs>
65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 87 <conditional name="query_fasta">
66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 88 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
67 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 89 <option value="none" selected="true">Do not provide query assemblies</option>
68 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> 90 <option value="collection">Query assemblies from a collection_type</option>
91 <option value="history">Query assemblies from your history</option>
92 </param>
93 <when value="none">
94 </when>
95 <when value="collection">
96 <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
97 </when>
98 <when value="history">
99 <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" />
100 </when>
101 </conditional>
102
103 <conditional name="ref_fasta">
104 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
105 <option value="none" selected="true">Do not provide reference assemblies</option>
106 <option value="collection">Reference assemblies from a collection_type</option>
107 <option value="history">Reference assemblies from your history</option>
108 </param>
109 <when value="none">
110 </when>
111 <when value="collection">
112 <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
113 </when>
114 <when value="history">
115 <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" />
116 </when>
117 </conditional>
118 <conditional name="query_reads">
119 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
120 <option value="none" selected="true">Do not provide query reads</option>
121 <option value="collection">Query reads from a collection_type</option>
122 <option value="history">Query reads from your history</option>
123 </param>
124 <when value="none">
125 </when>
126 <when value="collection">
127 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
128 </when>
129 <when value="history">
130 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
131 </when>
132 </conditional>
133
134 <conditional name="ref_reads">
135 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
136 <option value="none" selected="true">Do not provide reference reads</option>
137 <option value="collection">Refrence reads from a collection_type</option>
138 <option value="history">Refrence reads from your history</option>
139 </param>
140 <when value="none">
141 </when>
142 <when value="collection">
143 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
144 </when>
145 <when value="history">
146 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
147 </when>
148 </conditional>
69 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> 149 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
70 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> 150 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
71 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 151 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
72 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 152 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
73 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> 153 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />