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comparison tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 13:623f727cdff1 draft

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Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
author peterjc
date Fri, 14 Mar 2014 07:40:46 -0400
parents 4c4a0da938ff
children 2fe07f50a41e
comparison
equal deleted inserted replaced
12:6560192c5098 13:623f727cdff1
1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.22"> 1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.00">
2 <description>Make BLAST database</description> 2 <description>Make BLAST database</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">makeblastdb</token> 4 <token name="@BINARY@">makeblastdb</token>
5 <import>ncbi_macros.xml</import> 5 <import>ncbi_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command interpreter="python">check_no_duplicates.py 8 <command interpreter="python">check_no_duplicates.py
9 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so) 9 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)
10 ##and abort (via the ampersand ampersand trick) if any are found. 10 ##and abort (via the ampersand ampersand trick) if any are found.
11 #for $i in $in 11 #for i in $input_file#"${i}" #end for#
12 "${i.file}"
13 #end for
14 &amp;&amp; 12 &amp;&amp;
15 makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" 13 makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
16 $parse_seqids 14 $parse_seqids
17 $hash_index 15 $hash_index
18 ## Single call to -in with multiple filenames space separated with outer quotes 16 ## Single call to -in with multiple filenames space separated with outer quotes
19 ## (presumably any filenames with spaces would be a problem). Note this gives 17 ## (presumably any filenames with spaces would be a problem). Note this gives
20 ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy: 18 ## some extra spaces, e.g. -in "file1 file2 file3 " but BLAST seems happy:
21 -in " 19 -in "#for i in $input_file#${i} #end for#"
22 #for $i in $in
23 ${i.file}
24 #end for
25 "
26 #if $title: 20 #if $title:
27 -title "$title" 21 -title "$title"
28 #else: 22 #else:
29 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful 23 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
30 -title "BLAST Database" 24 -title "BLAST Database"
31 #end if 25 #end if
32 -dbtype $dbtype 26 -dbtype $dbtype
33 #set $mask_string = '' 27 ## --------------------------------------------------------------------
34 #set $sep = '-mask_data ' 28 ## Masking
35 #for $i in $mask_data 29 ## --------------------------------------------------------------------
36 #set $mask_string += $sep + str($i.file) 30 ## HACK: If no mask files, evaluates as a list with just None in it:
37 #set $sep = ',' 31 ## See Trello issue https://trello.com/c/lp5YmA1O
32 #if ' '.join( map(str, $mask_data_file) ) != 'None':
33 #for i in $mask_data_file:
34 -mask_data "${i}"
38 #end for 35 #end for
39 $mask_string 36 #end if
40 ## #set $gi_mask_string = '' 37 ## --------------------------------------------------------------------
41 ## #set $sep = '-gi_mask -gi_mask_name ' 38 ## Taxonomy
42 ## #for $i in $gi_mask 39 ## --------------------------------------------------------------------
43 ## #set $gi_mask_string += $sep + str($i.file) 40 #if $tax.taxselect == 'id':
44 ## #set $sep = ',' 41 -taxid $tax.taxid
45 ## #end for 42 ## TODO - Can we use a tabular file for the taxonomy mapping?
46 ## $gi_mask_string 43 ## #else if $tax.taxselect == 'map':
47 ## #if $tax.select == 'id': 44 ## -taxid_map $tax.taxmap
48 ## -taxid $tax.id 45 #end if
49 ## #else if $tax.select == 'map':
50 ## -taxid_map $tax.map
51 ## #end if
52 ## -------------------------------------------------------------------- 46 ## --------------------------------------------------------------------
53 ## Capture the stdout log information to the primary file (plain text): 47 ## Capture the stdout log information to the primary file (plain text):
54 &gt;&gt; "$outfile" 48 &gt; "$outfile"
55 </command> 49 </command>
56 <expand macro="stdio" /> 50 <expand macro="stdio" />
57 <inputs> 51 <inputs>
58 <param name="dbtype" type="select" display="radio" label="Molecule type of input"> 52 <param name="dbtype" type="select" display="radio" label="Molecule type of input">
59 <option value="prot">protein</option> 53 <option value="prot">protein</option>
60 <option value="nucl">nucleotide</option> 54 <option value="nucl">nucleotide</option>
61 </param> 55 </param>
62 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) 56 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)?
63 NOTE Double check the new database would be self contained first 57 NOTE Double check the new database would be self contained first
64 <repeat name="in" title="BLAST or FASTA Database" min="1">
65 <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" />
66 </repeat>
67 --> 58 -->
68 <!-- TODO Switch this to using <param ... multiple="true" /> instead of <repeat> block? --> 59 <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->
69 <repeat name="in" title="FASTA file" min="1"> 60 <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />
70 <param name="file" type="data" format="fasta" />
71 </repeat>
72 <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> 61 <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />
73 <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> 62 <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
74 <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> 63 <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />
75 <!-- SEQUENCE MASKING OPTIONS --> 64 <!-- SEQUENCE MASKING OPTIONS -->
76 <repeat name="mask_data" title="Masking data file"> 65 <!-- Note this is an optional parameter - default should be NO files -->
77 <param name="mask_data_file" type="data" format="maskinfo-asn1,maskinfo-asn1-binary" label="ASN.1 file containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> 66 <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />
78 </repeat> 67 <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? -->
79 <!-- TODO
80 <repeat name="gi_mask" title="Create GI indexed masking data">
81 <param name="gi_mask_file" type="data" format="asnb" label="Masking data output file" />
82 </repeat>
83 -->
84
85 <!-- TAXONOMY OPTIONS --> 68 <!-- TAXONOMY OPTIONS -->
86 <!-- TODO
87 <conditional name="tax"> 69 <conditional name="tax">
88 <param name="select" type="select" label="Taxonomy options"> 70 <param name="taxselect" type="select" label="Taxonomy options">
89 <option value="">Do not assign sequences to Taxonomy IDs</option> 71 <option value="">Do not assign a Taxonomy ID to the sequences</option>
90 <option value="id">Assign all sequences to one Taxonomy ID</option> 72 <option value="id">Assign the same Taxonomy ID to all the sequences</option>
73 <!--
91 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> 74 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option>
75 -->
92 </param> 76 </param>
93 <when value=""> 77 <when value="">
94 </when> 78 </when>
95 <when value="id"> 79 <when value="id">
96 <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer &gt;=0" /> 80 <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" help="Integer &gt;=0, e.g. 9606 for Homo sapiens" min="0" />
97 </when> 81 </when>
82 <!-- TODO: File format?
98 <when value="map"> 83 <when value="map">
99 <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> 84 <param name="taxmap" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />
100 </when> 85 </when>
86 -->
101 </conditional> 87 </conditional>
102 -->
103 </inputs> 88 </inputs>
104 <outputs> 89 <outputs>
105 <!-- If we only accepted one FASTA file, we could use its human name here... --> 90 <!-- If we only accepted one FASTA file, we could use its human name here... -->
106 <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> 91 <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}">
107 <change_format> 92 <change_format>
110 </change_format> 95 </change_format>
111 </data> 96 </data>
112 </outputs> 97 </outputs>
113 <tests> 98 <tests>
114 <!-- Note the (two line) PIN file is not reproducible run to run. 99 <!-- Note the (two line) PIN file is not reproducible run to run.
100 Likewise there is a datestamp in the log file as well, so use contains comparison
101 With and without the masking makes no difference.
102 With and without the taxid the only real difference is in the *.phr file.
115 --> 103 -->
116 <test> 104 <test>
117 <param name="dbtype" value="prot" /> 105 <param name="dbtype" value="prot" />
118 <param name="file" value="four_human_proteins.fasta" ftype="fasta" /> 106 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
119 <param name="title" value="Just 4 human proteins" /> 107 <param name="title" value="Just 4 human proteins" />
120 <param name="parse_seqids" value="" /> 108 <param name="parse_seqids" value="" />
121 <param name="hash_index" value="true" /> 109 <param name="hash_index" value="true" />
122 <output name="out_file" file="four_human_proteins.fasta.log" ftype="blastdbp" lines_diff="6"> 110 <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
111 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
112 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
113 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
114 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" />
115 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" />
116 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" />
117 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" />
118 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" />
119 </output>
120 </test>
121 <test>
122 <param name="dbtype" value="prot" />
123 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
124 <param name="title" value="Just 4 human proteins" />
125 <param name="parse_seqids" value="" />
126 <param name="hash_index" value="true" />
127 <param name="taxselect" value="id" />
128 <param name="taxid" value="9606" />
129 <output name="out_file" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">
130 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" />
131 <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" />
132 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" />
133 <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" />
134 <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" />
135 <extra_files type="file" value="four_human_proteins_taxid.fasta.phi" name="blastdb.phi" />
136 <extra_files type="file" value="four_human_proteins_taxid.fasta.psd" name="blastdb.psd" />
137 <extra_files type="file" value="four_human_proteins_taxid.fasta.psi" name="blastdb.psi" />
138 </output>
139 </test>
140 <test>
141 <param name="dbtype" value="prot" />
142 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
143 <param name="title" value="Just 4 human proteins" />
144 <param name="parse_seqids" value="" />
145 <param name="hash_index" value="true" />
146 <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" />
147 <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
123 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> 148 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
124 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> 149 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
125 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> 150 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
126 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> 151 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" />
127 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> 152 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" />