Mercurial > repos > galaxyp > blastxml_to_tabular_selectable
annotate blastxml_to_tabular_selectable.xml @ 1:5da5dcc5e13a default tip
Update from 24 to 25 columns and update versions to 1.0.0
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 08 Oct 2014 18:57:39 -0500 |
| parents | 2bd0cbccb3c6 |
| children |
| rev | line source |
|---|---|
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5da5dcc5e13a
Update from 24 to 25 columns and update versions to 1.0.0
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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1 <tool id="blastxml_to_tabular_selectable" name="BLAST XML to selected tabular columns" version="1.0.0"> |
| 0 | 2 <description>Convert BLAST XML output to tabular</description> |
| 3 <command interpreter="python"> | |
| 4 blastxml_to_tabular_selectable.py -o $tabular_file | |
| 5 #if $output.out_format == 'cols' and $output.columns: | |
| 6 -c '$output.columns' | |
| 7 #else | |
| 8 -c '$output.out_format' | |
| 9 #end if | |
| 10 $qdef | |
| 11 $allqueries | |
| 12 #if $unmatched: | |
| 13 -u $unmatched_file | |
| 14 #end if | |
| 15 #if $maxhits.__str__ != '': | |
| 16 --maxhits $maxhits | |
| 17 #end if | |
| 18 #if $maxhsps.__str__ != '': | |
| 19 --maxhsps $maxhsps | |
| 20 #end if | |
| 21 #for i in $blastxml_file#${i} #end for# | |
| 22 ## $blastxml_file | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> | |
| 26 <param name="qdef" type="boolean" truevalue="-d" falsevalue="" checked="False" label="Use Iteration_query-def value for qseqid"/> | |
| 27 <param name="allqueries" type="boolean" truevalue="-a" falsevalue="" checked="False" label="Output all queries including those with no hits"/> | |
| 28 <param name="unmatched" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Output a list with queries having no hits"/> | |
| 29 <param name="maxhits" type="integer" value="1" optional="true" label="Maximum number of Hits to display for a query"> | |
| 30 <validator type="in_range" min="1" /> | |
| 31 </param> | |
| 32 <param name="maxhsps" type="integer" value="1" optional="true" label="Maximum number of HSPs to display for a Hit"> | |
| 33 <validator type="in_range" min="1" /> | |
| 34 </param> | |
| 35 | |
| 36 <conditional name="output"> | |
| 37 <param name="out_format" type="select" label="Output format"> | |
| 38 <option value="std" selected="True">Tabular (standard 12 columns)</option> | |
|
1
5da5dcc5e13a
Update from 24 to 25 columns and update versions to 1.0.0
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
39 <option value="ext">Tabular (extended 25 columns)</option> |
| 0 | 40 <option value="cols">Tabular (select columns to output)</option> |
| 41 </param> | |
| 42 <when value="std"/> | |
| 43 <when value="ext"/> | |
| 44 <when value="cols"> | |
| 45 <param name="columns" type="select" multiple="true" display="checkboxes" label="Output columns"> | |
| 46 <option value="qseqid"> 1 qseqid Query Seq-id (ID of your sequence)</option> | |
| 47 <option value="sseqid"> 2 sseqid Subject Seq-id (ID of the database hit)</option> | |
| 48 <option value="pident"> 3 pident Percentage of identical matches</option> | |
| 49 <option value="length"> 4 length Alignment length</option> | |
| 50 <option value="mismatch"> 5 mismatch Number of mismatches</option> | |
| 51 <option value="gapopen"> 6 gapopen Number of gap openings</option> | |
| 52 <option value="qstart"> 7 qstart Start of alignment in query</option> | |
| 53 <option value="qend"> 8 qend End of alignment in query</option> | |
| 54 <option value="sstart"> 9 sstart Start of alignment in subject (database hit)</option> | |
| 55 <option value="send">10 send End of alignment in subject (database hit)</option> | |
| 56 <option value="evalue">11 evalue Expectation value (E-value)</option> | |
| 57 <option value="bitscore">12 bitscore Bit score</option> | |
| 58 <option value="sallseqid">13 sallseqid All subject Seq-id(s), separated by a ';'</option> | |
| 59 <option value="score">14 score Raw score</option> | |
| 60 <option value="nident">15 nident Number of identical matches</option> | |
| 61 <option value="positive">16 positive Number of positive-scoring matches</option> | |
| 62 <option value="gaps">17 gaps Total number of gaps</option> | |
| 63 <option value="ppos">18 ppos Percentage of positive-scoring matches</option> | |
| 64 <option value="qframe">19 qframe Query frame</option> | |
| 65 <option value="sframe">20 sframe Subject frame</option> | |
| 66 <option value="qseq">21 qseq Aligned part of query sequence</option> | |
| 67 <option value="sseq">22 sseq Aligned part of subject sequence</option> | |
| 68 <option value="qlen">23 qlen Query sequence length</option> | |
| 69 <option value="slen">24 slen Subject sequence length</option> | |
| 70 <option value="salltitles">25 salltitles = All subject title(s), separated by a '<>'</option> | |
| 71 </param> | |
| 72 </when> | |
| 73 </conditional> | |
| 74 </inputs> | |
| 75 <outputs> | |
| 76 <data name="tabular_file" format="tabular" label="BLAST results as tabular for ${on_string}" /> | |
| 77 <data name="unmatched_file" format="tabular" label="Query sequences with no hits for ${on_string}"> | |
| 78 <filter>unmatched == True</filter> | |
| 79 </data> | |
| 80 </outputs> | |
| 81 <requirements> | |
| 82 </requirements> | |
| 83 <tests> | |
| 84 <test> | |
| 85 <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" /> | |
| 86 <param name="out_format" value="std" /> | |
| 87 <output name="tabular_file" file="blastp_rhodopsin_proteins_std.tabular" ftype="tabular" /> | |
| 88 </test> | |
| 89 <test> | |
| 90 <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" /> | |
| 91 <param name="out_format" value="ext" /> | |
| 92 <output name="tabular_file" file="blastp_rhodopsin_proteins_ext.tabular" ftype="tabular" /> | |
| 93 </test> | |
| 94 <test> | |
| 95 <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" /> | |
| 96 <param name="out_format" value="cols" /> | |
| 97 <param name="columns" value="qseqid,sseqid,length,bitscore" /> | |
| 98 <output name="tabular_file" file="blastp_rhodopsin_proteins_selcol.tabular" ftype="tabular" /> | |
| 99 </test> | |
| 100 <test> | |
| 101 <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" /> | |
| 102 <param name="out_format" value="ext" /> | |
| 103 <param name="maxhits" value="10" /> | |
| 104 <param name="maxhsps" value="10" /> | |
| 105 <output name="tabular_file" file="blastp_rhodopsin_proteins_ext_allhits.tabular" ftype="tabular" /> | |
| 106 </test> | |
| 107 <test> | |
| 108 <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" /> | |
| 109 <param name="out_format" value="ext" /> | |
| 110 <param name="maxhits" value="1" /> | |
| 111 <param name="maxhsps" value="1" /> | |
| 112 <param name="unmatched" value="True" /> | |
| 113 <param name="allqueries" value="True" /> | |
| 114 <output name="tabular_file" file="blastp_rhodopsin_proteins_ext_allqueries.tabular" ftype="tabular" /> | |
| 115 <output name="unmatched_file" file="unmatched_queries.tabular" ftype="tabular" /> | |
| 116 </test> | |
| 117 </tests> | |
| 118 <help> | |
| 119 | |
| 120 **What it does** | |
| 121 | |
| 122 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of | |
| 123 formats including tabular and a more detailed XML format. A complex workflow | |
| 124 may need both the XML and the tabular output - but running BLAST twice is | |
| 125 slow and wasteful. | |
| 126 | |
| 127 This tool takes the BLAST XML output and by default converts it into the | |
| 128 standard 12 column tabular equivalent: | |
| 129 | |
| 130 ====== ========= ============================================ | |
| 131 Column NCBI name Description | |
| 132 ------ --------- -------------------------------------------- | |
| 133 1 qseqid Query Seq-id (ID of your sequence) | |
| 134 2 sseqid Subject Seq-id (ID of the database hit) | |
| 135 3 pident Percentage of identical matches | |
| 136 4 length Alignment length | |
| 137 5 mismatch Number of mismatches | |
| 138 6 gapopen Number of gap openings | |
| 139 7 qstart Start of alignment in query | |
| 140 8 qend End of alignment in query | |
| 141 9 sstart Start of alignment in subject (database hit) | |
| 142 10 send End of alignment in subject (database hit) | |
| 143 11 evalue Expectation value (E-value) | |
| 144 12 bitscore Bit score | |
| 145 ====== ========= ============================================ | |
| 146 | |
| 147 The BLAST+ tools can optionally output additional columns of information, | |
| 148 but this takes longer to calculate. Most (but not all) of these columns are | |
| 149 included by selecting the extended tabular output. The extra columns are | |
| 150 included *after* the standard 12 columns. This is so that you can write | |
| 151 workflow filtering steps that accept either the 12 or 22 column tabular | |
| 152 BLAST output. | |
| 153 | |
| 154 ====== ============= =========================================== | |
| 155 Column NCBI name Description | |
| 156 ------ ------------- ------------------------------------------- | |
| 157 13 sallseqid All subject Seq-id(s), separated by a ';' | |
| 158 14 score Raw score | |
| 159 15 nident Number of identical matches | |
| 160 16 positive Number of positive-scoring matches | |
| 161 17 gaps Total number of gaps | |
| 162 18 ppos Percentage of positive-scoring matches | |
| 163 19 qframe Query frame | |
| 164 20 sframe Subject frame | |
| 165 21 qseq Aligned part of query sequence | |
| 166 22 sseq Aligned part of subject sequence | |
| 167 23 qlen Query sequence length | |
| 168 24 slen Subject sequence length | |
| 169 25 salltitles All subject title(s), separated by a '<>' | |
| 170 ====== ============= =========================================== | |
| 171 | |
| 172 Beware that the XML file (and thus the conversion) and the tabular output | |
| 173 direct from BLAST+ may differ in the presence of XXXX masking on regions | |
| 174 low complexity (columns 21 and 22), and thus also calculated figures like | |
| 175 the percentage idenity (column 3). | |
| 176 | |
| 177 </help> | |
| 178 </tool> |