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comparison csp2_screen.xml @ 42:bbbf36187d87

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 14:15:42 -0500
parents e48f693bac6f
children 32ee1ce20411
comparison
equal deleted inserted replaced
41:e48f693bac6f 42:bbbf36187d87
4 <requirement type="package" version="24.10.1">nextflow</requirement> 4 <requirement type="package" version="24.10.1">nextflow</requirement>
5 <requirement type="package" version="1.5.8">micromamba</requirement> 5 <requirement type="package" version="1.5.8">micromamba</requirement>
6 </requirements> 6 </requirements>
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 export CSP2_DIR=\$PWD; 9
10 mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; 10 mkdir -p ./queries ./references &&
11 11
12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
13 #for query in $query_fasta: 13 #for query in $query_fasta:
14 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; 14 ln -sf ${query} ./queries/${query.element_identifier} &&
15 #end for 15 #end for
16 export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; 16 export QUERY_FASTA_ARG="--fasta ./queries" &&
17 else 17 else
18 export QUERY_FASTA_ARG=""; 18 export QUERY_FASTA_ARG="" &&
19 fi; 19 fi &&
20 20
21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
22 #for query in $query_reads: 22 #for query in $query_reads:
23 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; 23 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier} &&
24 #end for 24 #end for
25 export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; 25 export QUERY_READS_ARG="--reads \$CSP2_DIR/queries" &&
26 else 26 else
27 export QUERY_READS_ARG=""; 27 export QUERY_READS_ARG="" &&
28 fi; 28 fi &&
29 29
30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
31 #for ref in $ref_fasta: 31 #for ref in $ref_fasta:
32 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; 32 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
33 #end for 33 #end for
34 export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; 34 export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references" &&
35 else 35 else
36 export REF_FASTA_ARG=""; 36 export REF_FASTA_ARG="" &&
37 fi; 37 fi &&
38 38
39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
40 #for ref in $ref_reads: 40 #for ref in $ref_reads:
41 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; 41 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
42 #end for 42 #end for
43 export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; 43 export REF_READS_ARG="--ref_reads \$CSP2_DIR/references" &&
44 else 44 else
45 export REF_READS_ARG=""; 45 export REF_READS_ARG="" &&
46 fi; 46 fi &&
47 47
48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
49 export TRIM_ARG="--trim_name $trim_name"; 49 export TRIM_ARG="--trim_name $trim_name" &&
50 else 50 else
51 export TRIM_ARG=""; 51 export TRIM_ARG="" &&
52 fi; 52 fi &&
53 53
54 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then 54 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
55 export REF_ID_ARG="--ref_id $ref_id"; 55 export REF_ID_ARG="--ref_id $ref_id" &&
56 else 56 else
57 export REF_ID_ARG=""; 57 export REF_ID_ARG="" &&
58 fi; 58 fi &&
59 59
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_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; 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 &&
61 cat Nextflow_Log.txt; 61 cat Nextflow_Log.txt &&
62 ]]> 62 ]]>
63 </command> 63 </command>
64 <inputs> 64 <inputs>
65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />