# HG changeset patch
# User iuc
# Date 1490174611 14400
# Node ID 30775c836c7757458412925b268eb0eaf859cf44
# Parent  26b7446bb17e2be91b42f666878ae8f2d6ec2031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ee50324111351323cc294e051a6fab1733a89ec1

diff -r 26b7446bb17e -r 30775c836c77 fastq_dump.xml
--- a/fastq_dump.xml	Wed Dec 07 09:10:29 2016 -0500
+++ b/fastq_dump.xml	Wed Mar 22 05:23:31 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Extract reads" version="@VERSION@">
+<tool id="fastq_dump" name="Extract reads" version="@VERSION@.1">
     <description>in FASTQ/A format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -93,20 +93,19 @@
     ;
 
 
-    #if str( $outputformat ) == "fasta":
-
-        for f in *_2.fasta ; do   mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ;  mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta"  ; done &&
-        for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
-
-    #else:
-
-        for f in *_2.fastq ; do   mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ;  mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq"  ; done &&
-        for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
-
-    #end if
 
 
 
+    for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do
+      count=`ls \$i* | wc -l` ;
+      data=(\$(ls -d \$i*));
+      
+      if [ "\$count" -eq 2 ]; then
+         mv "\${data[0]}" "\${data[0]}"_forward.$outputformat;  mv "\${data[1]}" "\${data[1]}"_reverse.$outputformat ;
+      elif [ "\$count" -eq 1 ]; then
+         mv "\${data[0]}" "\${data[0]}"__single.$outputformat ;
+      fi;
+    done
 
 
     #end if
@@ -153,13 +152,13 @@
              identifier in the nested collection and identifier_1 is either
              forward or reverse (for instance samp1_forward.fq).
         -->
-        <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" ext="fastqsanger" visible="false" />
-        <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fasta" ext="fasta" visible="false" />
+        <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fastq_(?P&lt;identifier_1&gt;[^_]+)\.fastq" ext="fastqsanger" visible="false" />
+        <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fasta_(?P&lt;identifier_1&gt;[^_]+)\.fasta" ext="fasta" visible="false" />
       </collection>
       <collection name="output_collection" type='list' label="Single-end Fast(q|a)">
         <filter>input['input_select'] == "file_list"</filter>
-        <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastq" directory="." ext='fastqsanger'/>
-        <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fasta" directory="." ext='fasta'/>
+        <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fastq__single\.fastq" directory="." ext='fastqsanger'/>
+        <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fasta__single\.fasta" directory="." ext='fasta'/>
       </collection>
       <data format="fastqsanger" name="output_accession" >
         <filter>input['input_select'] == "accession_number"</filter>
@@ -194,6 +193,43 @@
         <param name="maxID" value="5"/>
         <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/>
       </test>
+      <test>
+        <param name="input_select" value="file_list"/>
+        <param name="outputformat" value="fastqsanger"/>
+        <param name="file_list" value="list_pe"/>
+        <param name="maxID" value="5"/>
+        <output_collection name="list_paired" type="list:paired">
+          <element name="DRR015708">
+            <element name="forward" file="DRR015708_forward.fastqsanger">
+            </element>
+            <element name="reverse" file="DRR015708_reverse.fastqsanger">
+            </element>
+          </element>
+        </output_collection>
+      </test>
+      <test>
+        <param name="input_select" value="file_list"/>
+        <param name="outputformat" value="fastqsanger"/>
+        <param name="file_list" value="list_pe2"/>
+        <param name="maxID" value="5"/>
+        <output_collection name="list_paired" type="list:paired">
+          <element name="ERR027433">
+            <element name="forward" file="ERR027433_forward.fastqsanger">
+            </element>
+            <element name="reverse" file="ERR027433_reverse.fastqsanger">
+            </element>
+          </element>
+        </output_collection>
+      </test>      
+      <test>
+        <param name="input_select" value="file_list"/>
+        <param name="outputformat" value="fastqsanger"/>
+        <param name="file_list" value="list_se"/>
+        <param name="maxID" value="5"/>
+        <output_collection name="output_collection" type="list">
+          <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
+        </output_collection>
+      </test>            
     </tests>
     <help>
         This tool extracts reads from SRA archives using fastq-dump.
diff -r 26b7446bb17e -r 30775c836c77 test-data/DRR015708_forward.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DRR015708_forward.fastqsanger	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,20 @@
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1
+NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT
++DRR015708.1 HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938 length=100
+#1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2<?<CC
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1
+NTTCTAAACTCATTCCAGAAGTAATTGATGCGTCACCAATAATTGCAATATGTTTTCTATTGATTTGATTGATTTTATCTGCTGTTGCCATCCCAACAAT
++DRR015708.2 HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930 length=100
+#4=DDFFFHHHHHJJJJJJIIHIJJJJJJJJIHJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJIIIICHHGEHHGIFEHHHHFFDFFFDDCEB@AC
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1
+NTCACCTACAACTCGAATATTCGAATGATATGTGATATTGTTAGATGATTTTGGCATGCTTGCAGAAAGTGCATAAACACCTGTATTGATTCCCGAATTT
++DRR015708.3 HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936 length=100
+#4=DFFFFHHHHHIJIJJIHIIJIIJJJJIJIHIIGGIIJHIEHGGHGHIIJJJIIJJJJJHHCHGGGE@FHGHIIJIEHHEDCCDCCDEEED@AB/=A#
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1
+NCTTAAAACTTATTAAATGAATCAATTAGATAAAAGACTTTTTTTGTTAGATGCTTATGCCTTAATTTTTAGAGGATATTATGCATTTATCAAAAATCCA
++DRR015708.4 HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864 length=100
+#4=DFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIHGDGHIJJJJJJGHHJGIJIJJJJJJJIJIJJJJJHFFHGFDDFEEFEECCEEDEEDDCC3<A5>C
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1
+NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC
++DRR015708.5 HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887 length=100
+#1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC
diff -r 26b7446bb17e -r 30775c836c77 test-data/DRR015708_reverse.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DRR015708_reverse.fastqsanger	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,20 @@
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2
+CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT
++DRR015708.1 HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938 length=100
+CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58<?BD:#+2?@?#########
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2
+GAAAGATGGTATTTCTGGTTTTCCAACGCGTACAGAAAGTGAGTTTGATACATTTGGAACGGGACATTCTTCTACATCTATTTCAGCAATTGTTGGGATG
++DRR015708.2 HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930 length=100
+BBCFFDFFHCFHHJJJJJIJJJJJJJIJJJJJJJIHGIIDHGIFIIJIIGHIIHIIJDHIIJH=DFFFFFEEEEEDEDDDEDEDDDDDCDDDCDDDBBDB
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2
+AAATATAATTGGAGAATCAACTTTATTTTCGAATACAATTCCAAATCAAAAAGAAGATAAAACACTAGAATTATCTCAAAAGAATTCAACTCAAAAAGAT
++DRR015708.3 HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936 length=100
+CCCFFFFFHHHHGJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJEIJJJJHIJJIJJJIJJJIJJIJJJIJIJJJHHHGEHFFDFF>C@C>CEC;A538:
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2
+ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT
++DRR015708.4 HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864 length=100
+CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2
+TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT
++DRR015708.5 HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887 length=100
+BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD
diff -r 26b7446bb17e -r 30775c836c77 test-data/ERR027433_forward.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR027433_forward.fastqsanger	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,20 @@
+@IL4_4847:5:1:1051:7109/1
+GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT
++ERR027433.1 IL4_4847:5:1:1051:7109 length=62
+C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B#######
+@IL4_4847:5:1:1058:16093/1
+AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC
++ERR027433.2 IL4_4847:5:1:1058:16093 length=62
+?ABBABB;<@>@=<?@CBBB:@2>BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1
+@IL4_4847:5:1:1111:15034/1
+TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT
++ERR027433.3 IL4_4847:5:1:1111:15034 length=62
+2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)########
+@IL4_4847:5:1:1122:6048/1
+ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT
++ERR027433.4 IL4_4847:5:1:1122:6048 length=62
+BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@<AA4:A3'@9+4;&00'9+AC5--DA5,?
+@IL4_4847:5:1:1138:20693/1
+CTGCTCGCGCGAGAACGCGCGCAAGCTCGGGGGCGGTGGCGGGGTCGGGCGACACCGATGTA
++ERR027433.5 IL4_4847:5:1:1138:20693 length=62
+CB<C7@>);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C##
diff -r 26b7446bb17e -r 30775c836c77 test-data/ERR027433_reverse.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR027433_reverse.fastqsanger	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,20 @@
+@IL4_4847:5:1:1051:7109/3
+AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA
++ERR027433.1 IL4_4847:5:1:1051:7109 length=54
+)(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'(
+@IL4_4847:5:1:1058:16093/3
+GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG
++ERR027433.2 IL4_4847:5:1:1058:16093 length=54
+;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$
+@IL4_4847:5:1:1111:15034/3
+GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG
++ERR027433.3 IL4_4847:5:1:1111:15034 length=54
+::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<(
+@IL4_4847:5:1:1122:6048/3
+GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG
++ERR027433.4 IL4_4847:5:1:1122:6048 length=54
+=8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.&
+@IL4_4847:5:1:1138:20693/3
+TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT
++ERR027433.5 IL4_4847:5:1:1138:20693 length=54
+;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3
diff -r 26b7446bb17e -r 30775c836c77 test-data/SRR1993644.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1993644.fastqsanger	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,20 @@
+@1/2
+TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC
++SRR1993644.1 1 length=101
+?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3>
+@2/2
+AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT
++SRR1993644.2 2 length=101
+<@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?#
+@3/2
+GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA
++SRR1993644.3 3 length=101
+=BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD
+@4/2
+TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT
++SRR1993644.4 4 length=101
+BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE
+@5/2
+ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT
++SRR1993644.5 5 length=101
+BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
diff -r 26b7446bb17e -r 30775c836c77 test-data/list_pe
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list_pe	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,1 @@
+DRR015708
diff -r 26b7446bb17e -r 30775c836c77 test-data/list_pe2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list_pe2	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,1 @@
+ERR027433
diff -r 26b7446bb17e -r 30775c836c77 test-data/list_se
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list_se	Wed Mar 22 05:23:31 2017 -0400
@@ -0,0 +1,1 @@
+SRR1993644