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Added support for a comment column in the SIFT tool

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This commit is contained in:
Richard Burhans
2010-11-19 15:20:51 -05:00
parent 54a002917f
commit 9a0205cfe4
2 changed files with 29 additions and 6 deletions
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tools/human_genome_variation/sift.xml
+16 -4
View File
@@ -2,7 +2,7 @@
<description>predictions of functional sites</description>
<command interpreter="bash">
sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$output_opts"
sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$comment_source.comment_col" "$output_opts"
</command>
<inputs>
@@ -13,12 +13,12 @@
<param name="chrom_col" type="data_column" data_ref="input" label="Column with chromosome"/>
<param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
<param name="base" type="select" label="Position coordinates are">
<option value="0">zero-based</option>
<option value="1" selected="true">one-based</option>
<option value="0">zero-based</option>
</param>
<param name="allele_col" type="data_column" data_ref="input" label="Column with allele"/>
<conditional name="strand_source">
<param name="choice" type="select" label="Strand info">
<param name="strand_choice" type="select" label="Strand info">
<option value="data_column" selected="true">a column in the dataset</option>
<option value="all_pos">all on sense/forward/+ strand</option>
<option value="all_neg">all on antisense/reverse/- strand</option>
@@ -33,6 +33,18 @@
<param name="strand_col" type="hidden" value="-"/>
</when>
</conditional>
<conditional name="comment_source">
<param name="comment_choice" type="select" label="Include comment column">
<option value="no" selected="true">no</option>
<option value="yes">yes</option>
</param>
<when value="no">
<param name="comment_col" type="hidden" value="-"/>
</when>
<when value="yes">
<param name="comment_col" type="data_column" data_ref="input" label="Column with comment"/>
</when>
</conditional>
<param name="output_opts" type="select" multiple="true" display="checkboxes" label="Include the following additional fields in the output">
<option value="A">Ensembl Gene ID</option>
<option value="B">Gene Name</option>
@@ -66,7 +78,7 @@
<param name="pos_col" value="3"/>
<param name="base" value="1"/>
<param name="allele_col" value="5"/>
<param name="choice" value="data_column"/>
<param name="strand_choice" value="data_column"/>
<param name="strand_col" value="4"/>
<param name="output_opts" value="A"/>
<output name="output" file="sift_variants_result.tab"/>
tools/human_genome_variation/sift_variants_wrapper.sh
+13 -2
View File
@@ -9,7 +9,8 @@ pos_col=$6
base=$7
allele_col=$8
strand_col=$9
output_opts=${10}
comment_col=${10}
output_opts=${11}
working_dir=$PWD
sift_input="$working_dir/sift_input.txt"
@@ -59,13 +60,23 @@ else
strand_cvt='if ( '"${strand}"' == "+") { '"${strand}"' = "1" } else if ( '"${strand}"' == "-") { '"${strand}"' = "-1"}'
fi
if [ "$comment_col" = "-" ]; then
is_comment=0
else
is_comment=1
fi
awk '
BEGIN {FS="\t";OFS=","}
{
$'"${chrom_col}"' = tolower($'"${chrom_col}"')
sub(/^chr/, "", $'"${chrom_col}"')
'"${strand_cvt}"'
print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'
if ('"${is_comment}"') {
print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"', $'"${comment_col}"'
} else {
print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'
}
}
' "$input_file" > "$sift_input"