changeset 3:72860740f65f draft

planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty

--- a/README.rst	Thu Mar 08 10:39:34 2018 -0500
+++ b/README.rst	Wed Mar 14 10:13:40 2018 -0400
@@ -17,7 +17,7 @@
 
 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. 
 
-If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs.
+If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. Please, note that a "NA" is returned when there is no corresponding ID.
 
 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
 
@@ -31,13 +31,13 @@
 
 * Entrez gene ID (e.g. 7529)
 
-* RefSeq (NCBI) protein (e.g.  NP_003395.1; NP_647539.1; XP_016883528.1)
+* RefSeq (NCBI) protein (e.g.  NP_003395.1)
 
-* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741)
+* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)
 
-* Protein DataBank ID (e.g. 2BR9:A; 3UAL:A;   3UBW:A)
+* Protein DataBank ID (e.g. 2BR9:A)
 
-* GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634)
+* GOterms (Gene Ontology) ID (e.g. GO:0070062)
 
 * Protein Information Resource ID (e.g. S34755)
 
@@ -47,14 +47,27 @@
 
 * Ensembl gene ID (e.g. ENSG00000166913)
 
-* Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839)
+* Ensembl transcript ID (e.g. ENST00000353703)
 
-* Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930)
+* Ensembl protein ID (e.g. ENSP00000300161)
+
+-----
 
-This tool converts human IDs using file built from:
+.. class:: infomark
 
-* HUMAN_9606_idmapping_selected.tab
+This tool converts human IDs using the following source files:
+
+* HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
     Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
 
-* nextprot_ac_list_all.txt 
-    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
\ No newline at end of file
+* nextprot_ac_list_all.txt (Nextprot released on 01/08/2017)
+    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
+
+-----
+
+.. class:: warningmark
+
+Accession numbers with an hyphen ("-") that normally correspond to isoform are considered 
+(and will therefore be treated) as similar to its canonical form.
+
+For example, "Q71U36-2" will be treated as "Q71U36".

--- a/id_converter.xml	Thu Mar 08 10:39:34 2018 -0500
+++ b/id_converter.xml	Wed Mar 14 10:13:40 2018 -0400
@@ -43,7 +43,7 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
-                <param name="ncol" type="text" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
             </when>
         </conditional>
 	    <conditional name="idti" >
@@ -176,10 +176,10 @@
 
 This tool converts human IDs using the following source files:
 
-* HUMAN_9606_idmapping_selected.tab
+* HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
     Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
 
-* nextprot_ac_list_all.txt 
+* nextprot_ac_list_all.txt (Nextprot released on 01/08/2017)
     Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
 
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