Repository 'rnaspades'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/rnaspades

Changeset 0:0d30fed9628b (2016-12-13)
Next changeset 1:9e58ff014088 (2017-03-28)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
added:
rnaspades.xml
test-data/rnaspades-in1-1.fq
test-data/rnaspades-in1-2.fq
test-data/rnaspades-out1.fa
b
diff -r 000000000000 -r 0d30fed9628b rnaspades.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaspades.xml Tue Dec 13 11:32:10 2016 -0500
[
@@ -0,0 +1,134 @@
+<tool id="rnaspades" name="rnaSPAdes" version="3.9.0">
+    <description>assembler for RNA-Seq data</description>
+    <requirements>
+        <requirement type="package" version="3.9.0">spades</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[
+        rnaspades.py -o .
+        ## Forces unzipped output, faster
+        --disable-gzip-output
+        $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent
+        ## Sequence files, libraries
+        #for $i, $library in enumerate( $libraries, start=1 ):
+            #if str( $library.lib_type ) == "paired_end":
+                #set prefix = 'pe'
+            #elif str( $library.lib_type ) == "mate_paired":
+                #set prefix = 'mp'
+            #elif str( $library.lib_type ) == "nxmate_paired":
+                #set prefix = 'nxmate'
+            #else:
+                #set prefix = 'hqmp'
+            #end if
+            --$prefix$i-$library.orientation
+            #for $file in $library.files
+                #if $file.file_type.type == "separate":
+                    --$prefix$i-1 fastq:$file.file_type.fwd_reads
+                    --$prefix$i-2 fastq:$file.file_type.rev_reads
+                #elif $file.file_type.type == "interleaved":
+                    --$prefix$i-12 fastq:$file.file_type.interleaved_reads
+                #elif $file.file_type.type == "unpaired":
+                    --$prefix$i-s fastq:$file.file_type.unpaired_reads
+                #elif $file.file_type.type == "paired-collection":
+                    --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
+                    --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
+                #end if
+            #end for
+        #end for
+        #for $contig in $trusted_contigs:
+            #if $contig:
+                --trusted-contigs $contig.extension:$contig
+            #end if
+        #end for
+        #for $contig in $untrusted_contigs:
+            #if $contig:
+                --untrusted-contigs $contig.extension:$contig
+            #end if
+        #end for
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--draft-assembly" checked="False" falsevalue="" label="Draft assembly. Faster, but more error-prone" name="draft" truevalue="--draft-assembly" type="boolean" />
+        <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
+        <param argument="--iontorrent" checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
+        <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries">
+            <param label="Library type" name="lib_type" type="select">
+                <option value="paired_end">Paired-end / Single reads</option>
+                <option value="mate_paired">Mate pairs</option>
+                <option value="high_mate_paired">High Quality Mate pairs</option>
+                <option value="nxmate_paired">Lucigen NxMate pairs</option>
+            </param>
+            <param label="Orientation" name="orientation" type="select">
+                <option selected="true" value="fr">-&gt; &lt;- (fr)</option>
+                <option value="rf"><![CDATA[<- -> (rf)]]></option>
+                <option value="ff"><![CDATA[-> -> (ff)]]></option>
+            </param>
+            <repeat min="1" name="files" title="Files">
+                <conditional name="file_type">
+                    <param label="Select file format" name="type" type="select">
+                        <option value="separate">Separate input files</option>
+                        <option value="interleaved">Interleaved files</option>
+                        <option value="unpaired">Unpaired/Single reads</option>
+                        <option value="paired-collection">Paired List Collection</option>
+                    </param>
+                    <when value="separate">
+                        <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
+                        <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
+                    </when>
+                    <when value="interleaved">
+                        <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
+                    </when>
+                    <when value="unpaired">
+                        <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
+                    </when>
+                    <when value="paired-collection">
+                        <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
+                    </when>
+                </conditional>
+            </repeat>
+        </repeat>
+        <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
+        <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
+    </inputs>
+    <outputs>
+        <data format="fasta" label="rnaSPAdes transcripts" name="output_transcripts" from_work_dir="transcripts.fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="lib_type" value="paired_end" />
+            <param name="type" value="separate" />
+            <param name="fwd_reads" value="rnaspades-in1-1.fq" ftype="fastq" />
+            <param name="rev_reads" value="rnaspades-in1-2.fq" ftype="fastq" />
+            <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
+
+This wrapper runs SPAdes 3.9.0, collects the output, and throws away all the temporary files.
+
+**License**
+
+SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
+
+The original wrapper was written by Lionel Guy, Philip Mabon and was released under the GNU General Public License as published by the Free Software Foundation. The rnaSPAdes extension was developed by the Galaxy team.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+
+** Acknowledgments **
+
+Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
+
+Nicola Soranzo fixed various bugs.
+    </help>
+    <citations>
+        <citation type="doi">10.1089/cmb.2012.0021</citation>
+    </citations>
+</tool>
b
diff -r 000000000000 -r 0d30fed9628b test-data/rnaspades-in1-1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaspades-in1-1.fq Tue Dec 13 11:32:10 2016 -0500
b
b'@@ -0,0 +1,4000 @@\n+@KM034562v1_16634_17111_3:0:0_1:0:0_0/1\n+AAAAGTAAGGCACCAGCACCTTCTCCCTCTGCCAGCGTCACAGCCGACTTAAAATTCTCTATTTCCCAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14097_14553_2:0:0_2:0:0_1/1\n+AGTCCTACGTACAATCTGGCGCAGACATGAAGTTAAGTCTTGCGACCCAGGAACATTTCATCCGCTAGGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16925_17343_3:0:0_2:0:0_2/1\n+AAACCCAAGATGAGATATGAAAGTACTTACTGCAATTGAGATCCTTCATTGATACCACAGTTTATTGTAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16067_16623_0:0:0_2:0:0_3/1\n+CTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_13552_14038_2:0:0_2:0:0_4/1\n+GTTAAGCATGTTTTTAATTGGATGCATTATACAATCCCCCAGTGTTATATGCATGTCAGTGATTATTATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_18264_18791_3:0:0_1:0:0_5/1\n+ACATACAGATTATAAAAAACTCATAAATTGCTCTCATCCATCATCTTGAACTGCTTTCAATAAATAACTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_1343_1836_2:0:0_4:0:0_6/1\n+GAGTATGCTCCTTTCGCCCGACTTTTGAAGCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5492_5996_3:0:0_0:0:0_7/1\n+GGTTATCCAATTGAAAAGGACCTGATGACCCCTACTCTGGAAGACAAATAATCTAAGAGAGATGAAGATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_18170_18666_2:0:0_2:0:0_8/1\n+AGGGTATCACCATTTTTAAATCGACAAATTAAAGCAATGACAATTATAAAAAACTTAATCTTAAAGATGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_8524_9042_2:0:0_1:0:0_9/1\n+CGTCATCACAGCACATAGAGTTAACCATGCCCTTAATTTGGAATCCTCTATGGTTCGGATGTCTTGTCTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14751_15266_2:0:0_1:0:0_a/1\n+ACCCATGTTAAACGGGACGCCAATTCAATGGCGTCTCTTAAGGCTGCGGAAGGACATTTTGGTTTAATAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6159_6697_3:0:0_1:0:0_b/1\n+AGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACCAATCAAATGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14330_14670_0:0:0_3:0:0_c/1\n+CTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5470_6001_1:0:0_2:0:0_d/1\n+ATTTTGGTTATCCAATTGAAAAGGACCTGATGACCCCTACTCTGGAAGACAAATACTCTAAGAGAGCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16843_17293_2:0:0_4:0:0_e/1\n+CAAATAATCTCCCATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14376_14891_1:0:0_3:0:0_f/1\n+GTTATATGGTTTAAAGCCTCCTCCAGGATATTATCACAATGATCAAGATAACTAAACCATAGACTCCACC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10335_10778_2:0:0_0:0:0_10/1\n+CGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCGCAAAAAGGACCTGGAGAAAGGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_7962_8527_0:0:0_1:0:0_11/1\n+ACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2472_3023_3:0:0_3:0:0_12/1\n+TTTCTTAATTATAAACCGAACGTGAAAATGTTGGGCAGGCTAGTAGGTAAGTTATAAAAGCATAATGTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_8516_9029_1:0:0_2:0:0_13/1\n+CATAGAGTTAACAATGCCCTTAATATGGAATCCTCTATGGTTCGGAAGTCTTGTCTCGCCCAGTGTTCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11256_11765_1:1:0_0:0:0_14/1\n+AACTTGGTAACAGTTACATCATATTTTAAACGGTATATATGTTTCGGGAGTTTACAGTTGCGTAGTTGCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11405_11937_1:0:0_0:0:0_15/1\n+'..b'222222222222222222222222222222\n+@KM034562v1_5709_6237_2:0:0_2:0:0_3d3/1\n+CAACTGATCTCACTTGATTTGTGGATGACAGTTTGTCACGACAAACTCGTTTGTCGACATCACTAACCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10974_11435_0:0:0_5:0:0_3d4/1\n+CCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5615_6005_0:0:0_3:0:0_3d5/1\n+GCTAATTTTGTTTATCCAATTGAAAAGGACCTGATGACCCCTACTCTGGAAGACACATAATCTAAGAGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_348_795_1:0:0_0:0:0_3d6/1\n+TTGACTTCAAAACGGAACCCGTGCCCTTCCAAATACTTGACTGCGCCACTTTCCAAGAAAAGTTTGTAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2183_2701_2:0:0_1:0:0_3d7/1\n+TTACATGCTCATTCACTGATGATTTTGCAGGATTGCCATGAATTTATTCCTGTGATTCATTACTGGCCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12181_12742_1:0:0_0:0:0_3d8/1\n+AACACACAAGGAATCCCCCATGCTGGTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15967_16405_1:1:0_2:0:0_3d9/1\n+GGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTACCTTGGCAATACAATTCTTCGGAGTAAGAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15154_15743_1:0:0_2:0:0_3da/1\n+CCATACATTGGATCAAGGACAGAAGATAAGATAGGGCAACCTGGTATTAAACCAAAATGTCCTTCCGCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_1195_1647_2:0:0_0:0:0_3db/1\n+AGGTCTATTGATTGTCAAAACCGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTGTCCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10521_11040_1:0:0_1:0:0_3dc/1\n+TTGTGTAAATGCTTTCAGTGTGGACTCATGAAGGAGGGAAAATTTCGCCGGGCCAGGCTTCTTGCGGTTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_7862_8291_4:0:0_0:0:0_3dd/1\n+CATCAAGTTTATCATTCTTAAAGATATAGCTAGATTGATGTCAAACCTTGTTTATGATTAACTGTGAGTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_4669_5237_2:0:0_2:0:0_3de/1\n+ATCAATTGGAACGATCTAAAAGTCCTGGAGTGAAGTCATTATTGCTTGGATTATCTCCGGAGATGTTAGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12684_13204_3:0:0_0:0:0_3df/1\n+ATTTTCCAAACAAAAACACTGGTGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAACAGTTAAAAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12207_12636_0:0:0_2:0:0_3e0/1\n+TATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2001_2466_1:0:0_3:0:0_3e1/1\n+GTCAAAAGGGCCAGCATACAGAGGGCAGACATACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11421_11925_1:0:0_0:0:0_3e2/1\n+TGTTAGGTTTCCCAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAAGTAGGTTAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6860_7417_1:0:0_1:1:0_3e3/1\n+TTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAACAACCTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16758_17339_1:0:0_0:0:0_3e4/1\n+AGCAAACCCAAAACTAAAATTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_17437_17962_2:0:0_2:0:0_3e5/1\n+CTAGTTTTGTGATTCGTCCTTTTGCAGTACGAATAAAGTGCTATGTTTGAGTCCGACTATGTCGCTGTTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15492_15999_2:0:0_3:0:0_3e6/1\n+ACTTACAAAGGCCCCAAAACTGTACAGCAGACCTATCTTGGGATAAGTTAAGAAAAGGGTAGTGAATGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6156_6644_2:0:0_3:0:0_3e7/1\n+AATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACCAACTGTCATCCACAAATCCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n'
b
diff -r 000000000000 -r 0d30fed9628b test-data/rnaspades-in1-2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaspades-in1-2.fq Tue Dec 13 11:32:10 2016 -0500
b
b'@@ -0,0 +1,4000 @@\n+@KM034562v1_16634_17111_3:0:0_1:0:0_0/2\n+ATGGCAGTGAACGGAGTGTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCCCAAGAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14097_14553_2:0:0_2:0:0_1/2\n+AATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTGCTTGCAGAATAACCGCAGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16925_17343_3:0:0_2:0:0_2/2\n+GACTTGCCTAGGTAGCCTTGCTCTTTTGTCTTTAAACCAAGTAGGATTAGTTATGTCTGTTATTTGGCTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16067_16623_0:0:0_2:0:0_3/2\n+TCTGGTGGTTTGTTCTTGACTTCTCTTAATATGACCATCACTGTTGTTTGTGCTTGCTCCAGTAGAAGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_13552_14038_2:0:0_2:0:0_4/2\n+TAGCCGTTTTAAGGGACTTAGGCAATTGGACCCCATACAAATATTGTTTTTTTCCAAAATAGATAAAACC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_18264_18791_3:0:0_1:0:0_5/2\n+GAAGGTATTTCTGATTTTACAGTCATGTCTTTTCTTTTAATTTTATCATTCTGAAAGGAATAGTAGCTTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_1343_1836_2:0:0_4:0:0_6/2\n+TCGGTAATGGTCGTATCCTGTGAGTCAGTCGGATCATCATCTTTATGGCCAGTATTTTCGTCATCATTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5492_5996_3:0:0_0:0:0_7/2\n+AATCTTCTCAGGGATAGTGATAACATCTTTTAAATAATCCGTCTACTATAAGAGATACTTCTAATTGATG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_18170_18666_2:0:0_2:0:0_8/2\n+TGACAGGGCTTCTGAGTTTATTTCCAGATGGTCTCTCCAGGTTCGATAGAATAACCGTGCATAGTATTTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_8524_9042_2:0:0_1:0:0_9/2\n+GATAGAGGACGCCCCCGAGCTGCCAGACATCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14751_15266_2:0:0_1:0:0_a/2\n+AGCCTCTACGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAATATAACATTGCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6159_6697_3:0:0_1:0:0_b/2\n+TATCTAATTGTGGTAGAATAATAGCCACTCGACGGGTCCTCCGTTGCATTGACCGGCTCTGTCAAGGGGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14330_14670_0:0:0_3:0:0_c/2\n+GAAACGACTCAAAAGAGGAGTTGATGATAAGAGCCACTTACAAACCAATTCGTCTTCGAAGTCAGCTGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5470_6001_1:0:0_2:0:0_d/2\n+TGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATATTGATAACATCTTTTTAATAATCCGTCTACTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16843_17293_2:0:0_4:0:0_e/2\n+ATATGTCTGTAATATGGCTTGCTGAGTTGTTAAGAATAATCTGAATTTGGTCATTATGGAATTTTGACAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_14376_14891_1:0:0_3:0:0_f/2\n+TTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGCTGATTTATTCTTACCTTTAATTGCGAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10335_10778_2:0:0_0:0:0_10/2\n+AATTGTTCCTTGACACGTTGTGTTCGCATGTTGAAATGGTTAGTGTTGGTTGTTAGCAGCCAATCAGAGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_7962_8527_0:0:0_1:0:0_11/2\n+TCTCATATGAAGCTTCCATTTAAGAGTTGTCTGCACTCACTGATTAAATTTCTATTGACTTTTTTACCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2472_3023_3:0:0_3:0:0_12/2\n+ATCATATTATGAAGGATGAGCCTGTAGTTTTCATTACCAGTGAAGGTAAAGAGTACACGTATCCGGACTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_8516_9029_1:0:0_2:0:0_13/2\n+CTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGCCCACCATGTTCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11256_11765_1:1:0_0:0:0_14/2\n+CCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGTATCCCTCAAATAAGAGATTCCAAGACAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11405_11937_1:0:0_0:0:0_15/2\n+'..b'222222222222222222222222222222\n+@KM034562v1_5709_6237_2:0:0_2:0:0_3d3/2\n+AGGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCCAATTGCCTACATGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10974_11435_0:0:0_5:0:0_3d4/2\n+TTGTGAAACCTAACACAGATGACCTGCGGGTTTAGTTACAAATAACCAATACGTATAATGGATTTCTAGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_5615_6005_0:0:0_3:0:0_3d5/2\n+CTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_348_795_1:0:0_0:0:0_3d6/2\n+GAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCCACAACCCTAAAGCCTGGGGTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2183_2701_2:0:0_1:0:0_3d7/2\n+CTGGACTATGCCGACGACGAGACGTCTAGGCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12181_12742_1:0:0_0:0:0_3d8/2\n+TTTGGATTGCTGTTTCACTATGTAGCACAGGATGCCCCCAGTGTTTTTGTATGGAAAATAGCTCACAAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15967_16405_1:1:0_2:0:0_3d9/2\n+CCTGGTGTCTTGATGAATCATGCACCAGCAGTTCTACGATCTGATTGAGGAAATTATTAACAGGTGTTTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15154_15743_1:0:0_2:0:0_3da/2\n+CCTTTTAGAGGAATATTGTCATAAATCAATTCATTTTCTCGGTATCTTGATAAATCTAAATCCAATGTAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_1195_1647_2:0:0_0:0:0_3db/2\n+GCGTTTGTTTGCTGGAAGCTGATTTCGTTCTTTTTCTGATGGAAGTTCATAAGAATTTTCTTTTCCTGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_10521_11040_1:0:0_1:0:0_3dc/2\n+ACTGAAAACTAATGCCTTTGCCCCTGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_7862_8291_4:0:0_0:0:0_3dd/2\n+TGTATCGAACCACATGATTGGACCCAGACCATAACAGACAAAATTGATCAGATTATTGATGATTATGTTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_4669_5237_2:0:0_2:0:0_3de/2\n+ACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAATCTATGGTGAATGTCATATCGGGGCCCAAAGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12684_13204_3:0:0_0:0:0_3df/2\n+GTAGATACTCGAGTTTTTGCGCGTAGGAAAGAACATTCTCAATAGAAAAGTTTTCTTGCTCTAAAAATTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_12207_12636_0:0:0_2:0:0_3e0/2\n+ATGTAATTCACGGATCTTGTGAGCCTGTGAAGGCTTTAGTTCACGTATTTCTGTAATTTCTTCCAGGGTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_2001_2466_1:0:0_3:0:0_3e1/2\n+ACAACGGCATCAAATGGCCCCTGTGATCTTAGAATGAGGCGATACATCTCCTCAAAAGACTGTTCTGGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_11421_11925_1:0:0_0:0:0_3e2/2\n+TTTCAGGAAGAGAGCATCTTGCATTGTGTACTTAATAATTTCATCTAAGAACTGTTGGCACCGCGGCTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6860_7417_1:0:0_1:1:0_3e3/2\n+TCCAGCAGTCTCGCTGTAGTTTTGGGGGCTTGTCGTGGTGGCGCGGTCCAGGGAGTCAGCGCTCTTACTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_16758_17339_1:0:0_0:0:0_3e4/2\n+TGCCTAGGTAGCCTTGCTCTTTGGTCTTTAAACCAAGTAGGATTTGTTATGTCTGTTATTTGGCTTGCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_17437_17962_2:0:0_2:0:0_3e5/2\n+CCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGAATTTTATGGCTAAATG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_15492_15999_2:0:0_3:0:0_3e6/2\n+AGGTGGCCCATGGGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@KM034562v1_6156_6644_2:0:0_3:0:0_3e7/2\n+CGGCTGTCTCAAGGGGTGTGAGCTGAAGAAGTCCTTCTAAGCTTGGGGCAGTATGAGAAATGCAACGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n'
b
diff -r 000000000000 -r 0d30fed9628b test-data/rnaspades-out1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaspades-out1.fa Tue Dec 13 11:32:10 2016 -0500
b
@@ -0,0 +1,122 @@
+>NODE_1_length_193_cov_2.51449
+CATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCAT
+CATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAA
+AATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAG
+ATTTCATAGTTCC
+>NODE_2_length_186_cov_2.1374
+GTTCCAATTTCAATACTGCTCAATAATCCATTGTAGTTCACGACATGTAGAGCATCCAAT
+TTGTTAATAAACTTGAGAATATTGGATCGAATCAACGACAGCATTTTTAGGCTCAATTGT
+TCCTTGACACGTTGTGTTCGCATGTTGAAATGGTTAGTGTTGGTTGTTAGCAGCCAATCA
+GAGATC
+>NODE_3_length_181_cov_3.33333
+TTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCA
+TAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCA
+CAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTC
+A
+>NODE_4_length_178_cov_2.80488
+GCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTG
+TTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACA
+ACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTATCTCAGCAACGCG
+>NODE_5_length_156_cov_2.07921
+CATGCCGTTTTACGAGTAACTTTGGTATTCGCCGTAGCCTCCATCATCGGGGTCAACTAC
+CACATCGGGAATGGTCGTATCCTGTGAGTCAGTCGGATCATCATCTTGATGGCCAGGATT
+GTCGTCATCATTGATGGGTCCTGGAAAGGGAATGTC
+>NODE_6_length_153_cov_2
+GTGGGCGTCCTCTCTCATATGAAGCTTCCATTTAAGAGTTGTCTGCACTCACTGTTTAAA
+TTTCTATTGACTTTTTTACCAATGCTTTGTGTGTGTTAGGTTACAACTAAATTCTACCGG
+TTTGCAGATCTGATTATTACAACTTAAGAAAAA
+>NODE_7_length_153_cov_2.42857
+GAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGC
+ATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCT
+TGCTATCTAACTAAGATGGACTACTTCATATTG
+>NODE_8_length_151_cov_2.125
+TGAGTCCTCCTTTTAGAGGATTATTGTCATAAATCAATTCATTTTCTCGGTATCTTGTTA
+AATCTAAATCCAATGTAGATGTGTATGTTAAGTACTGAGCTGGTACCTCCCGGGTGCAAC
+ACTTAGTTAGATGAAGTTGAGCACGATTATA
+>NODE_9_length_149_cov_2.54255
+AACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACA
+GTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGA
+TGAAGATTAAGAAAAAGGTAATCTGTCGA
+>NODE_10_length_143_cov_2.55682
+GTTTGTTTTTCGCACTTAGGGTGATAGTCCTACGTACAATCTGGCGCAGAAATGAAGTTA
+AGTCTTGCGACCCAGGAACATTTAATCCGCTAGGATTTAGCACAAAGTCAATGGCAGTGC
+AGTTCCCAGGGTTCTTCGCAATT
+>NODE_11_length_137_cov_2.0122
+CCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCA
+GGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTAT
+GATCGACTTGCTTCCAC
+>NODE_12_length_134_cov_2.05063
+CTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACC
+ACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAA
+GGAGCGCCTCACAA
+>NODE_13_length_133_cov_3.01282
+ACGACAAACTAGTTTGTCGACATCACTAACCTGTAATGTACTATTGTGGATAACTCCAAG
+CGGGATGGAAAATGTTCTTTGGAAAAGGATAATTACCCAAAGAAAGAATGATGTCCTCTT
+GACTGGATCACGA
+>NODE_14_length_132_cov_2.41558
+GATGAAATTGCTGGCTGTACTCTTACATGTGTAAACAAGATTGTCGTGAGGATGTACATG
+ATCATTTATGGTAGTTTTAAAAGCCTGGTGTCTTGATGAATCATGCACCAGCAGTTCTAC
+GATCTGATGGAG
+>NODE_15_length_129_cov_2.21622
+CCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGAT
+GAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAA
+TGTCAATCT
+>NODE_16_length_128_cov_3.27397
+TTATCTTGGTTGTTTAATTGACTTATATTATCTAGGGCTGATACTCACAAGTGTATCATT
+AATGTAACATACCCTATAGTTCAGCAGTTGAAGCCTCTGCTATTAGTTGCCTCTTTCGGA
+GGGAAAAG
+>NODE_17_length_126_cov_2
+GAAATCCAAGATACGAAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTT
+TCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAAGTAGGTGAA
+GAAAAA
+>NODE_18_length_124_cov_2.47826
+TTTTTCCAAGGCTAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTA
+TCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCG
+TCGA
+>NODE_19_length_123_cov_2.13235
+ATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTT
+AAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATT
+CGA
+>NODE_20_length_121_cov_2.5
+GTCTCTGCATCCATGGTTATAACCTCGACTTGCCTAGGTAGCCTTGCTCTTTGGTCTTTA
+AACCAAGTAGGATTTGTTATGTCTGTTATTTGGCTTGCTGAGTTGTTAAGAATAATCTCA
+A
+>NODE_21_length_119_cov_2.1875
+ATCATTCACTACCCTTTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGC
+CTTTGTAAGTTATTACCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACA
+>NODE_22_length_117_cov_2.12903
+TCGTCGTCGGCATCGTCCAGTGGGTCTGCCTCTTCGTTGATTGGGGTCAGCATGCGAGGG
+CTGGTTGAGCCGGAGGGTTCGTTTCTTCTGTCATTGTCCGTGAGTGGAGCACAGGCA
+>NODE_23_length_113_cov_2.58621
+TCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAG
+GAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAG
+>NODE_24_length_113_cov_2.06897
+GATGATGAAGGTTTTAATCTTCATCATTAGTTTTTTCTTAATTATAAAACGATCGTGTAA
+ATGTTGGGCAGGCTAGTAGGTAAGTTATAAAAGCATAATGTAATTTAATTTAG
+>NODE_25_length_112_cov_2.52632
+ACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCT
+ATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTT
+>NODE_26_length_111_cov_2.51786
+AAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTC
+CTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCACTAGAGAACACG
+>NODE_27_length_110_cov_3.54545
+GCCATGATGCTTGATGCAATAAGCTTTCTTTTTGTTCACGTTCCGTAACTACCATCATAT
+TGCTAGGAAATGCTTTAGCAAGACCATCAGCTAACAGAGCTTCACAAAGT
+>NODE_28_length_110_cov_2.30909
+AGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACA
+ACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATG
+>NODE_29_length_109_cov_2.5
+CTTTCCATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGA
+AAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAAC
+>NODE_30_length_107_cov_2.59615
+ATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACC
+ATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGAT
+>NODE_31_length_107_cov_2.30769
+ATCCTAGTTTCATTGATTTGAGGTTGAGTTTTGCCGTGAAACAATCTGAAGAAAGACTAA
+AAGACAAATTTGCATATACAGAATAAAGCGATAACTGCAATTATAAC
+>NODE_32_length_107_cov_2.09615
+CCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAA
+TATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTT
+>NODE_33_length_105_cov_2.7
+ACCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTT
+AAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCAAGC