# HG changeset patch
# User saketkc
# Date 1397581206 14400
# Node ID 699ab41c6d764f072ebadb64538087ee93936d31
# Parent  84247b644a7d29e288d44d698f1f991c6ae5a32b
Uploaded

diff -r 84247b644a7d -r 699ab41c6d76 condel_web/condel_web.xml
--- a/condel_web/condel_web.xml	Mon Apr 14 21:37:22 2014 -0400
+++ b/condel_web/condel_web.xml	Tue Apr 15 13:00:06 2014 -0400
@@ -2,7 +2,9 @@
     <description>Condel web service</description>
     <requirements>
         <requirement type="package" version="2.2.1">requests</requirement>
+        <requirement type="package" version="7.19.3.1">pycurl</requirement>
         <requirement type="python-module">requests</requirement>
+        <requirement type="python-package">pycurl</requirement>
     </requirements>
     <command interpreter="python">
         condel_web.py --input $input --output $output
@@ -15,7 +17,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="condel_input.txt"/>
+            <param name="input" value="condel_input.tsv"/>
             <output name="output" file="condel_output.csv"/>
         </test>
     </tests>
@@ -36,6 +38,53 @@
         dataset of approximately 20000 missense SNPs, both deleterious and neutral. The probability that a predicted deleterious mutation is not a
         false positive of the method and the probability that a predicted neutral mutation is not a false negative are employed as weights.
 
+        **Input**
+
+        There are two main formats allowed:
+
+
+        SNVs may be submitted for analysis both in chromosome and protein coordinates.
+
+
+        The chromosome coordinates (hg19) input must follow this format:
+
+
+        [CHROMOSOME] [START] [END] [MUTANT_NUCLEOTIDE]
+
+
+
+        The END column is the same as the START for SNVs.
+        Those four columns must be separated by tabs. Also a fifth column can optionally be added with the Variant name
+
+
+        Ex:
+
+        9   32473058    32473058    A
+
+        7   43918688    43918688    C
+
+        Additionally, the input could be composed by two columns the strand of the SNV and an identifier:
+
+        [PROTEIN_ID][variant]
+
+        Also tab separated. Currently only Uniprot, RefSeq_Peptide and Ensembl identifiers are recognized by the webserver.
+
+        The variant column must contain the following information (in this order ): change_position, reference_aminoacid and changed_aminoacid
+
+        Ex:
+
+        EGFR_HUMAN R521K
+
+        EGFR_HUMAN R98Q
+
+        .. class:: warningmark
+
+        Note
+
+        Please, note that the Variant Effect Predictor assumes that the allele submitted is coded in the forward strand.
+
+        If you are assessing the effect of variants coded in the reverse strand, please introduce the complementary nucleotide instead.
+
         **Citation**
 
 
diff -r 84247b644a7d -r 699ab41c6d76 condel_web/test-data/condel_input.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/condel_web/test-data/condel_input.tsv	Tue Apr 15 13:00:06 2014 -0400
@@ -0,0 +1,5 @@
+9	32473058	32473058	A
+7	43918688	43918688	C
+7	38471790	38471790	A
+6	88372821	88372821	A
+5	41934236	41934236	G
diff -r 84247b644a7d -r 699ab41c6d76 condel_web/test-data/condel_input.txt
--- a/condel_web/test-data/condel_input.txt	Mon Apr 14 21:37:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-9	32473058	32473058	A
-7	43918688	43918688	C
-7	38471790	38471790	A
-6	88372821	88372821	A
-5	41934236	41934236	G
diff -r 84247b644a7d -r 699ab41c6d76 condel_web/tool_dependencies.xml
--- a/condel_web/tool_dependencies.xml	Mon Apr 14 21:37:22 2014 -0400
+++ b/condel_web/tool_dependencies.xml	Tue Apr 15 13:00:06 2014 -0400
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="requests" version="2.2.1">
-        <repository changeset_revision="570c2648d96d" name="package_requests_2_2_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="beautifulsoup4" version="4.1.0">
+        <repository changeset_revision="df0beb7ea718" name="package_beautifulsoup4_4_1_0" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pycurl" version="7.19.3.1">
+        <repository changeset_revision="9b02e8e36eff" name="package_pycurl_7_19_3_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>