Mercurial > repos > rliterman > csp2

comparison csp2_snp.xml @ 58:c8676ac8c6b7

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 12:19:14 -0500
parents c8dfcb29d91b
children d322910e773c
comparison
equal deleted inserted replaced
57:c8dfcb29d91b 58:c8676ac8c6b7
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 mkdir ./queries ./references; 9 mkdir ./queries ./references;
10 10
11 export QUERY_FASTA_SELECT="${query_fasta.query_fasta_select}" 11
12 export QUERY_READS_SELECT="${query_reads.query_reads_select}" 12 #set query_fasta_input=""
13 export REF_FASTA_SELECT="${ref_fasta.ref_fasta_select}" 13 #if $query_fasta.query_fasta_select == 'collection'
14 export REF_READS_SELECT="${ref_reads.ref_reads_select}" 14 #set query_fasta_input=$query_fasta.coll.elements
15 15 #elseif $query_fasta.query_fasta_select == 'history'
16 if [[ "\$QUERY_FASTA_SELECT" == "none" ]]; then 16 #set query_fasta_input=$query_fasta.list
17 #end if
18
19 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
17 export QUERY_FASTA_ARG=""; 20 export QUERY_FASTA_ARG="";
18 elif [[ "\$QUERY_FASTA_SELECT" == "history" ]]; then 21 else
19 #for query in $query_fasta.list: 22 #for query in $query_fasta_input:
20 ln -sf ${query} ./queries/${query.element_identifier}; 23 ln -sf ${query} ./queries/${query.element_identifier};
21 #end for 24 #end for
22 export QUERY_FASTA_ARG="--fasta ./queries"; 25 export QUERY_FASTA_ARG="--fasta ./queries";
23 else 26 fi;
24 #for query in $query_fasta.coll.elements: 27
28 #set ref_fasta_input=""
29 #if $ref_fasta.ref_fasta_select == 'collection'
30 #set ref_fasta_input=$ref_fasta.coll.elements
31 #elseif $ref_fasta.ref_fasta_select == 'history'
32 #set ref_fasta_input=$ref_fasta.list
33 #end if
34
35 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
36 export REF_FASTA_ARG="";
37 else
38 #for ref in $ref_fasta_input:
39 ln -sf ${ref} ./references/${ref.element_identifier};
40 #end for
41 export REF_FASTA_ARG="--fasta ./references";
42 fi;
43
44 #set query_reads_forward=""
45 #set query_reads_reverse=""
46 #if $query_reads.query_reads_select == 'collection'
47 #set query_reads_forward=$query_reads.coll.forward
48 #set query_reads_reverse=$query_reads.coll.revese
49 #elseif $query_reads.query_reads_select == 'history'
50 #set query_reads_forward=$query_reads.list
51 #set query_reads_reverse=""
52 #end if
53
54 if [[ "$query_reads.query_reads_select" == "none" ]]; then
55 export QUERY_READS_ARG="";
56 else
57 #for query in $query_reads_forward $query_reads_reverse:
25 ln -sf ${query} ./queries/${query.element_identifier}; 58 ln -sf ${query} ./queries/${query.element_identifier};
26 #end for 59 #end for
27 export QUERY_FASTA_ARG="--fasta ./queries"; 60 export QUERY_READS_ARG="--reads ./queries";
28 fi; 61 fi;
29 62
30 if [[ "\$REF_FASTA_SELECT" == "none" ]]; then 63 #set ref_reads_forward=""
31 export REF_FASTA_ARG=""; 64 #set ref_reads_reverse=""
32 elif [[ "\$REF_FASTA_SELECT" == "history" ]]; then 65 #if $ref_reads.ref_reads_select == 'collection'
33 #for ref in $ref_fasta.list: 66 #set ref_reads_forward=$ref_reads.coll.forward
67 #set ref_reads_reverse=$ref_reads.coll.revese
68 #elseif $ref_reads.ref_reads_select == 'history'
69 #set ref_reads_forward=$ref_reads.list
70 #set ref_reads_reverse=""
71 #end if
72
73 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
74 export QUERY_READS_ARG="";
75 else
76 #for ref in $ref_reads_forward $ref_reads_reverse:
34 ln -sf ${ref} ./references/${ref.element_identifier}; 77 ln -sf ${ref} ./references/${ref.element_identifier};
35 #end for 78 #end for
36 export REF_FASTA_ARG="--ref_fasta ./references";
37 else
38 #for ref in $ref_fasta.coll.elements:
39 ln -sf ${ref} ./references/${ref.element_identifier};
40 #end for
41 export REF_FASTA_ARG="--ref_fasta ./references";
42 fi;
43
44 if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
45 export QUERY_READS_ARG="";
46 elif [[ "\$QUERY_READS_SELECT" == "history" ]]; then
47 #for query in $query_reads.list:
48 ln -sf ${query} ./queries/${query.element_identifier};
49 #end for
50 export QUERY_READS_ARG="--reads ./queries"; 79 export QUERY_READS_ARG="--reads ./queries";
51 else
52 #for query in $query_reads.coll.forward:
53 ln -sf ${query} ./queries/${query.element_identifier};
54 #end for
55 #for query in $query_reads.coll.reverse:
56 ln -sf ${query} ./queries/${query.element_identifier};
57 #end for
58 export QUERY_READS_ARG="--reads ./queries";
59 fi;
60
61 if [[ "\$REF_READS_SELECT" == "none" ]]; then
62 export REF_READS_ARG="";
63 elif [[ "\$REF_READS_SELECT" == "history" ]]; then
64 #for ref in $ref_reads.list:
65 ln -sf ${ref} ./references/${ref.element_identifier};
66 #end for
67 export REF_READS_ARG="--ref_reads ./references";
68 else
69 #for ref in $ref_reads.coll.forward:
70 ln -sf ${ref} ./references/${ref.element_identifier};
71 #end for
72 #for ref in $ref_reads.coll.reverse:
73 ln -sf ${ref} ./references/${ref.element_identifier};
74 #end for
75 export REF_READS_ARG="--ref_reads ./references";
76 fi; 80 fi;
77 81
78 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then 82 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then
79 export TRIM_ARG="--trim_name $trim_name"; 83 export TRIM_ARG="--trim_name $trim_name";
80 else 84 else