Mercurial > repos > caleb-easterly > validate_fasta_database

changeset 4:e5a59fabeeba draft

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planemo upload commit e412b2a32af63a1a6dfcfcda5ad66ada0e1cd954-dirty
author caleb-easterly
date Wed, 28 Jun 2017 13:34:56 -0400
parents d45b2b8177a1
children d4bd627618e5
files FastaHeader-1.0-SNAPSHOT-jar-with-dependencies.jar FastaHeader-1.0-SNAPSHOT.jar validateFASTA.xml validate_fasta_headers.xml
diffstat 4 files changed, 20 insertions(+), 67 deletions(-) [+]
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Binary file FastaHeader-1.0-SNAPSHOT-jar-with-dependencies.jar has changed
Binary file FastaHeader-1.0-SNAPSHOT.jar has changed
--- a/validateFASTA.xml	Wed Jun 28 11:55:46 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-<tool id="validate_fasta_database" name="Validate FASTA Headers" version="0.1.1">
-    <requirements>
-    </requirements>
-    <stdio>
-        <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
-    </stdio>
-    <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/FastaHeader-1.0-SNAPSHOT-jar-with-dependencies.jar "$FASTA" "$goodFasta" "$badFasta" "$crashIfInvalid"  
-    ]]></command>
-    <inputs>
-        <param type="data" name="FASTA" format="fasta" label="Select input FASTA dataset"/>
-        <param type="boolean" name="crashIfInvalid" label="Fail job if invalid FASTA headers detected?"/>        
-    </inputs>
-    <outputs>
-        <data name="goodFasta" format="fasta" label="Validate FASTA: Passed Sequences"/>
-        <data name="badFasta" format="fasta" label="Validate FASTA: Failed Sequences"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="FASTA" value="fastaFilteringTest_IN.fasta"/>
-            <output name="goodFasta" file="fastaFilteringTest_OUT1.fasta" />
-            <output name="badFasta" file="fastaFilteringTest_OUT2.fasta" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-**Notes**
-
-Takes a FASTA database and validates the headers using the Compomics (developers of SearchGUI and PeptideShaker) schema. 
-Custom FASTA databases may be in an invalid format, which causes SearchGUI to crash.
-        
-**Output**
-
-The main output of this tool, "Validate FASTA: Passed Sequences", is a FASTA database that can be run through SearchGUI without error.
-The failed sequences may be examined for typos and other errors. 
-
-In addition, the tool will print the databases assigned by the Compomics utility (i.e., UniProt), for a quick check of the validity of the custom FASTA database. 
-
-Sequences that may cause the tool to report an exception are those that are not valid examples of the following formats: 
-    * UniProt,
-    * SwissProt (starts with ">sw|" or ">SW|")
-    * NCBI (starts with ">gi|" or ">GI|")
-    * Halobacterium from Max Planck (starts with "OE")
-    * H Influenza, from Novartis (starts with ">hflu_")
-    * C Trachomatis (starts with ">C.tr\_" or "C\_trachomatis\_")
-    * M Tuberculosis (starts with ">M. tub")
-    * Saccharomyces Genome Database (contains "SGDID")
-    * Genome translation (ex. ">dm345\_3L-sense [2343534-234353938]")
-    * Genome Annotation Framework for Flexible Analysis (GAFFA) (starts with ">GAFFA")
-    * UPS (contains "\_HUMAN\_UPS")
-           
-Many sequences are reported as Generic, which may or may not allow for extraction of the accession number. 
-]]>
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{fastaValidation,
-            author = {The GalaxyP Team},
-            date = {22 June 2017},
-            title = {FASTA Database Validation Tool}
-            }
-        </citation>
-    </citations>
-</tool>
--- a/validate_fasta_headers.xml	Wed Jun 28 11:55:46 2017 -0400
+++ b/validate_fasta_headers.xml	Wed Jun 28 13:34:56 2017 -0400
@@ -1,15 +1,32 @@
-<tool id="validate_fasta_database" name="Validate FASTA Headers" version="0.1.0">
+<tool id="validate_fasta_database" name="Validate FASTA Headers" version="0.1.1">
     <requirements>
     </requirements>
     <stdio>
         <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/FastaHeader-1.0-SNAPSHOT-jar-with-dependencies.jar "$FASTA" "$goodFasta" "$badFasta" "$crashIfInvalid"  
+        java -jar $__tool_directory__/FastaHeader-1.0-SNAPSHOT.jar '$FASTA' '$goodFasta' '$badFasta' '$crashIfInvalid'
+        '$checkIsProtein' $checkLength.checkLength
+        #if $checkLength.checkLength
+             $checkLength.minimumLength
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="FASTA" format="fasta" label="Select input FASTA dataset"/>
-        <param type="boolean" name="crashIfInvalid" label="Fail job if invalid FASTA headers detected?"/>        
+        <param type="boolean" name="crashIfInvalid" label="Fail job if invalid FASTA headers detected?"/>
+        <param type="boolean" name="checkIsProtein" label="Ensure that sequence is not DNA or RNA?"/>
+        <conditional name="checkLength">
+            <param type="boolean" name="checkLength" label="Filter out sequences below a minimum length?">
+                <option value="true"></option>
+                <option value="false"></option>
+            </param>
+            <when value="true">
+                <param name="minimumLength" type="integer" value="0" label="Minimum length that AA sequence must have"/>
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
+
     </inputs>
     <outputs>
         <data name="goodFasta" format="fasta" label="Validate FASTA: Passed Sequences"/>