# HG changeset patch
# User charles_s_test
# Date 1516919192 18000
# Node ID aca83a94fd55cb579bc33b3fc5c56051558ca197
# Parent  09e4f955e00a50033235f815e333cf01faafc480
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

diff -r 09e4f955e00a -r aca83a94fd55 aln-pe.sam
diff -r 09e4f955e00a -r aca83a94fd55 ectyper
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ectyper	Thu Jan 25 17:26:32 2018 -0500
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+
+"""
+    Shell program for ectyper
+"""
+import sys
+import os
+sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
+
+from ectyper import ectyper
+
+if __name__=='__main__':
+    ectyper.run_program()
diff -r 09e4f955e00a -r aca83a94fd55 ectyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ectyper.xml	Thu Jan 25 17:26:32 2018 -0500
@@ -0,0 +1,75 @@
+<tool id="ectyper" name="ectyper" version="0.1">
+    <requirements>
+      <requirement type="package" version="0.1">ectyper</requirement>
+      <requirement type="package" version="3.5">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      #if $jobtype.select == "asm"
+        ln -s $jobtype.draft sample.fasta;  
+      #else if $jobtype.select == "se"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+      #else if $jobtype.select == "pe"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq2 sample_2.fastq;  
+      #end if
+
+	  $__tool_directory__/ectyper 
+      #if $jobtype.select == "asm"
+        -i sample.fasta
+      #else if $jobtype.select == "se"
+        -i sample_1.fastq
+      #else if $jobtype.select == "pe"
+        -i sample_1.fastq sample_2.fastq
+      #end if
+      -d $percent_identity
+	  -l $percent_length
+  	  -o "./"; cat ./output/output.csv > results.csv; 
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="asm">Genome Assembly</option>
+          <option value="se">Single-End Reads</option>
+          <option value="pe">Paired-End Reads</option>
+        </param>
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+        </when>
+      </conditional>
+
+      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
+      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
+    
+    </inputs>
+    <outputs>
+            <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
+    </outputs>
+
+    <help><![CDATA[
+    
+**Usage: ectyper**
+
+**INPUT**
+
+A fasta assembly or single or paired end reads
+
+**PERCENTIDENTITY**
+
+Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
+
+**PERCENTLENGTH**
+
+Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
+
+https://github.com/phac-nml/ecoli_serotyping
+
+    ]]></help>
+</tool>
diff -r 09e4f955e00a -r aca83a94fd55 runfastq_dump.py
--- a/runfastq_dump.py	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-import sys, os
-
-input = sys.argv[1]
-
-print(input)
-
-import re, os
-
-def fix_seq_ids(filename):
-	'''
-	make sequence ids the same for paired reads.
-	'''
-	file = list(open(filename, 'r'))
-	new_file = open(filename, 'w')
-	for line in file:
-		if re.search('^@', line) or re.search('^\+', line) and re.search(' ', line):
-			linel = re.split(' ', line)
-			linel[0] = re.sub('.\d$', '', linel[0])
-			line = ' '.join(linel)
-		new_file.write(line)
-# fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
-
-os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump --log-level fatal --split-3 --accession ' + input + ' --ncbi_error_report never')
-
-os.system('ls -lh | grep ' + input)
-
-#os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump -I --split-files ' + input)
-#mv_cmd = 'mv -v ' + input + '_1.fastq R1.fastq'
-#print(mv_cmd)
-
-#fix_seq_ids(input + '_1.fastq')
-#fix_seq_ids(input + '_2.fastq')
-
-os.system('mv -v ' + input + '_1.fastq R1.fastq')
-os.system('mv -v ' + input + '_2.fastq R2.fastq')
-
-
-
diff -r 09e4f955e00a -r aca83a94fd55 test.bam
Binary file test.bam has changed
diff -r 09e4f955e00a -r aca83a94fd55 test.txt
--- a/test.txt	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Hello World
\ No newline at end of file
diff -r 09e4f955e00a -r aca83a94fd55 testdep.py
--- a/testdep.py	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
-import sys, os, io
-
-#input = sys.argv[1]
-
-print(input)
-
-import re, os
-
-def fix_seq_ids(filename):
-        '''
-        make sequence ids the same for paired reads.
-        '''
-        file = list(open(filename, 'r'))
-        new_file = open(filename, 'w')
-        for line in file:
-                if re.search('^@', line) or re.search('^\+', line) and re.search(' ', line):
-                        linel = re.split(' ', line)
-                        linel[0] = re.sub('.\d$', '', linel[0])
-                        line = ' '.join(linel)
-                new_file.write(line)
-# fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
-
-#os.system('bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat')
-os.system('samtools view -bS /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_472.dat > test.bam')
-
-os.system('blastx -query /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat -out output.blast.txt')
-
-
-file = open("test.txt","w") 
- 
-file.write("Hello World") 
- 
-file.close() 
-
-#os.system('/nfs/sw/apps/bwa/bwa-0.7.15/bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat')
-
-
-
-#os.system('bwa mem /nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/database/fliC_b_whole.fasta /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_445.dat /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_446.dat > aln-pe.sam')
-
-#os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump --log-level fatal --split-3 --accession ' + input + ' --ncbi_error_report never')
-
-#os.system('ls -lh | grep ' + input)
-
-#os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump -I --split-files ' + input)
-#mv_cmd = 'mv -v ' + input + '_1.fastq R1.fastq'
-#print(mv_cmd)
-
-#fix_seq_ids(input + '_1.fastq')
-#fix_seq_ids(input + '_2.fastq')
-
-#os.system('mv -v ' + input + '_1.fastq R1.fastq')
-#os.system('mv -v ' + input + '_2.fastq R2.fastq')
diff -r 09e4f955e00a -r aca83a94fd55 testdep.xml
--- a/testdep.xml	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-<tool id="testdep" name="Test Dep" version="1.1.4">
-    <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
-    <requirements>
-	<requirement type="package" version="0.5.9">bwa</requirement>  
-  	<requirement type="package" version="1.3.1">samtools</requirement>
-    	<requirement type="package" version="2.7.1">blast</requirement>
-        <requirement type="package" version="2.6.2">sra_toolkit</requirement>
-  </requirements>
-  <command interpreter="python2.7">    
-
-	testdep.py 
-
-   </command>
-    <inputs>
-      <param format="fastq,fastqsanger" name="input1" multiple="true" type="data" label="Source file"/>
-	</inputs>
-    <outputs>
-	 <data name="text_txt" format="txt" from_work_dir="test.txt"/>   
-
-	</outputs> 
-    <tests>
-         <test>    
-	<output name="text_txt" file="test.txt"/>
-	 </test>     
-    </tests>
-<help>
-
-.. class:: infomark
-
-**What it does**
-
-Performs a fastq-dump with the split-3 option.
-
-::
-
-  fastq-dump —log-level fatal --split-3 --accession accession_number --ncbi_error_report never
-
-
-Data is stored in format fastqsanger. 
-
-The metadata is now named to make it easier for collection lists to
-fetch when you search for reads in your history. 
-
-------
-
-.. class:: infomark
-
-Modifed By 
-Charles Strittmatter
-
-
-**Original Tool Author**
-
-Mando Rodriguez
-
-    </help>
-<citations>
-          <citation type="bibtex">
-          @Article{pmid25762776,
-               Author="Zhang, S.  and Yin, Y.  and Jones, M. B.  and Zhang, Z.  and Deatherage Kaiser, B. L.  and Dinsmore, B. A.  and Fitzgerald, C.  and Fields, P. I.  and Deng, X. ",
-                  Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
-                  Journal="J. Clin. Microbiol.",
-                  Year="2015",
-                  Volume="53",
-                  Number="5",
-                  Pages="1685--1692",
-                  Month="May"
-          }
-          </citation>
-     </citations>
-    
-</tool>
diff -r 09e4f955e00a -r aca83a94fd55 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bwa" version="0.5.9">
-        <repository changeset_revision="0eb3d3c40344" name="package_bwa_0_5_9" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
-