Mercurial > repos > nml > spades
annotate spades.xml @ 12:1796ea206dec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
| author | iuc |
|---|---|
| date | Thu, 16 Sep 2021 15:26:12 +0000 |
| parents | b8d633fbf5f5 |
| children | b7829778729f |
| rev | line source |
|---|---|
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1"> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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2 <description>genome assembler for regular and single-cell projects</description> |
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1796ea206dec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
iuc
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3 <xrefs> |
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1796ea206dec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
iuc
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4 <xref type="bio.tools">spades</xref> |
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1796ea206dec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
iuc
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5 </xrefs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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6 <macros> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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7 <import>macros.xml</import> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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8 </macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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9 <requirements> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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10 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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11 </requirements> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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12 <stdio> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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13 <exit_code range="1:" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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14 <regex match="Cannot allocate memory" |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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15 source="stdout" |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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16 level="fatal_oom" |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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17 description="Out of memory error occurred" /> |
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884dc0264950
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e
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18 <regex match="The reads contain too many k-mers to fit into available memory" |
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884dc0264950
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e
iuc
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19 source="stdout" |
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884dc0264950
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e
iuc
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20 level="fatal_oom" |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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21 description="Out of memory error occurred" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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22 </stdio> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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23 <command> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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24 <![CDATA[ |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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25 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
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26 |
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12
1796ea206dec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
iuc
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27 if [ -n "\$GALAXY_MEMORY_MB" ]; then |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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28 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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29 fi && |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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30 |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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31 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} |
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planemo upload commit ba4e93c036a072d6aac883bc1aba55e26256498c
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32 #if not $kmer_choice.auto_kmer_choice: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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33 -k "$kmer_choice.kmers" |
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planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753
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34 #end if |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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35 #if $cov.state == "auto": |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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36 --cov-cutoff 'auto' |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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37 #elif $cov.state == "value": |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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38 --cov-cutoff '$cov.cutoff' |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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39 #end if |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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40 $iontorrent |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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41 ## Sequence files, libraries |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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42 #for $i, $library in enumerate( $libraries, start=1 ) |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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43 #if str( $library.lib_type ) == "paired_end": |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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44 #set prefix = 'pe' |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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45 #elif str( $library.lib_type ) == "mate_paired": |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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46 #set prefix = 'mp' |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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47 #elif str( $library.lib_type ) == "nxmate_paired": |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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48 #set prefix = 'nxmate' |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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49 #else: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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50 #set prefix = 'hqmp' |
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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
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51 #end if |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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52 --$prefix$i-$library.orientation |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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53 #for $file in $library.files |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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54 #if $file.file_type.type == "separate" |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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55 --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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56 --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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57 #elif $file.file_type.type == "interleaved" |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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58 --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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59 #elif $file.file_type.type == "merged" |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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60 --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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61 #elif $file.file_type.type == "unpaired" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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62 --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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63 #elif $file.file_type.type == "paired-collection" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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64 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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65 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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66 #end if |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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67 #end for |
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68 #end for |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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69 #for $read in $pacbio_reads: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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70 #if $read: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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71 --pacbio fastq:$read |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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72 #end if |
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73 #end for |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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74 #for $read in $nanopore_reads: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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75 #if $read: |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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76 --nanopore fastq:$read |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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77 #end if |
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78 #end for |
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79 #for $read in $sanger_reads: |
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80 #if $read: |
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81 --sanger $read.extension.replace('fastqsanger', 'fastq'):$read |
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82 #end if |
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83 #end for |
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84 #for $contig in $trusted_contigs: |
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85 #if $contig: |
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86 --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig |
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87 #end if |
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88 #end for |
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89 #for $contig in $untrusted_contigs: |
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90 #if $contig: |
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91 --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig |
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92 #end if |
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93 #end for |
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94 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats' |
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95 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats' |
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96 ]]> |
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97 </command> |
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98 |
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99 <configfiles> |
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100 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python |
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101 import sys,re |
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102 search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$' |
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103 replace_str = r'\1_\2\t\3\t\4' |
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104 cmd = re.compile(search_str) |
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105 sys.stdout.write('#name\tlength\tcoverage\n') |
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106 for i,line in enumerate(sys.stdin): |
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107 if cmd.match(line): |
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108 sys.stdout.write(cmd.sub(replace_str,line)) |
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109 ]]> |
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110 </configfile> |
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111 </configfiles> |
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112 |
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113 <inputs> |
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114 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean"> |
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115 <option value="false">No</option> |
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116 <option value="true">Yes</option> |
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117 </param> |
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118 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" /> |
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119 <param argument="--careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" /> |
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120 <conditional name="kmer_choice"> |
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121 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" /> |
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122 <when value="false"> |
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123 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" /> |
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124 </when> |
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125 <when value="true" /> |
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126 </conditional> |
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127 <conditional name="cov"> |
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128 <param label="Coverage Cutoff" name="state" type="select"> |
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129 <option value="off">Off</option> |
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130 <option value="value">User Specific</option> |
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131 <option value="auto">Auto</option> |
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132 </param> |
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133 <when value="off" /> |
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134 <when value="value"> |
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135 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" /> |
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136 </when> |
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137 <when value="auto" /> |
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138 </conditional> |
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139 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" /> |
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140 <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" max="9" name="libraries" title="Libraries"> |
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141 <param label="Library type" name="lib_type" type="select"> |
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142 <option value="paired_end">Paired-end / Single reads</option> |
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143 <option value="mate_paired">Mate pairs</option> |
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144 <option value="high_mate_paired">High Quality Mate pairs</option> |
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145 <option value="nxmate_paired">Lucigen NxMate pairs</option> |
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146 </param> |
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147 <param label="Orientation" name="orientation" type="select"> |
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148 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option> |
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149 <option value="rf"><![CDATA[<- -> (rf)]]></option> |
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150 <option value="ff"><![CDATA[-> -> (ff)]]></option> |
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151 </param> |
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152 <repeat min="1" name="files" title="Files"> |
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153 <conditional name="file_type"> |
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154 <param label="Select file format" name="type" type="select"> |
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155 <option value="separate">Separate input files</option> |
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156 <option value="interleaved">Interleaved files</option> |
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157 <option value="merged">Merged files</option> |
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158 <option value="unpaired">Unpaired/Single reads</option> |
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159 <option value="paired-collection">Paired List Collection</option> |
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160 </param> |
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161 <when value="separate"> |
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162 <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" /> |
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163 <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" /> |
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164 </when> |
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165 <when value="interleaved"> |
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166 <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" /> |
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167 </when> |
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168 <when value="merged"> |
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169 <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" /> |
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170 </when> |
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171 <when value="unpaired"> |
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172 <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" /> |
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173 </when> |
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174 <when value="paired-collection"> |
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175 <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" /> |
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176 </when> |
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177 </conditional> |
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178 </repeat> |
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179 </repeat> |
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180 <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" /> |
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181 <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" /> |
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182 <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" /> |
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183 <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> |
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184 <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> |
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185 <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" /> |
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186 <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" /> |
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187 </inputs> |
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188 |
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189 <outputs> |
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190 <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" > |
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191 <actions> |
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192 <action name="column_names" type="metadata" default="name,length,coverage"/> |
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193 </actions> |
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194 </data> |
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195 <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" > |
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196 <actions> |
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197 <action name="column_names" type="metadata" default="name,length,coverage"/> |
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198 </actions> |
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199 </data> |
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200 <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" /> |
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201 <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" /> |
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202 <data format="txt" from_work_dir="spades.log" label="${tool.name} on ${on_string}: log" name="out_log" /> |
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203 <data format="txt" from_work_dir="assembly_graph.fastg" label="${tool.name} on ${on_string}: assembly graph" name="contig_graph"> |
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204 <filter>contig_graph_out</filter> |
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205 </data> |
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206 <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph"> |
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207 <filter>scaffold_graph_out</filter> |
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208 </data> |
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209 </outputs> |
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210 <tests> |
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211 <test> <!-- Test 1 - basic test with k=33 --> |
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212 <param name="sc" value="false" /> |
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213 <param name="careful" value="false" /> |
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214 <param name="kmers" value="33" /> |
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215 <param name="lib_type" value="paired_end" /> |
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216 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> |
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217 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> |
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218 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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219 <output name="out_contig_stats"> |
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220 <assert_contents> |
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221 <has_text_matching expression="NODE_1\t1000"/> |
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222 </assert_contents> |
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223 </output> |
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224 </test> |
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10
b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
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225 <test> <!-- Test 2 - basic test with k=33 fasta input --> |
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9
24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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226 <param name="sc" value="false" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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227 <param name="onlyassembler" value="true"/> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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228 <param name="careful" value="false" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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229 <param name="kmers" value="33" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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230 <param name="lib_type" value="paired_end" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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231 <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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232 <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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233 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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234 <output name="out_contig_stats"> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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235 <assert_contents> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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236 <has_text_matching expression="NODE_1\t1000"/> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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237 </assert_contents> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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238 </output> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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239 </test> |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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240 <test> <!-- Test 3 - basic test with k=33 and gzipped input --> |
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9
24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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241 <param name="sc" value="false" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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242 <param name="careful" value="false" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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243 <param name="kmers" value="33" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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244 <param name="lib_type" value="paired_end" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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245 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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246 <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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247 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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248 <output name="out_contig_stats"> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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249 <assert_contents> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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250 <has_text_matching expression="NODE_1\t1000"/> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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251 </assert_contents> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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252 </output> |
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24fffa4fee40
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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253 </test> |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
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254 <test> <!-- Test 4 - auto k --> |
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5
909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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255 <param name="sc" value="false" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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256 <param name="careful" value="false" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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257 <param name="auto_kmer_choice" value="true" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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258 <param name="lib_type" value="paired_end" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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259 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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260 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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261 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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262 </test> |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
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263 <test> <!-- Test 5 - k=77 --> |
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5
909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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264 <param name="sc" value="false" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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265 <param name="careful" value="false" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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266 <param name="kmers" value="77" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
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267 <param name="lib_type" value="paired_end" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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268 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> |
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909c315b656d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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269 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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270 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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909c315b656d
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271 </test> |
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b8d633fbf5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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272 <test> <!-- Test 6 - test for extra graph outputs --> |
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7
9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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273 <param name="sc" value="false" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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274 <param name="careful" value="false" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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275 <param name="kmers" value="33" /> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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276 <param name="lib_type" value="paired_end" /> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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277 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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278 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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279 <param name="contig_graph_out" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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280 <param name="scaffold_graph_out" value="true" /> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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281 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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282 <output name="out_contig_stats"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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283 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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284 <has_text_matching expression="NODE_1\t1000"/> |
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9006e5836729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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285 </assert_contents> |
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286 </output> |
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287 <output name="contig_graph"> |
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288 <assert_contents> |
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289 <has_text text=">EDGE_"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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290 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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291 </output> |
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292 <output name="scaffold_graph"> |
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293 <assert_contents> |
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294 <has_text text="NODE_"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
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295 </assert_contents> |
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296 </output> |
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297 </test> |
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298 <test> <!-- Test 7 - basic test with k=33 and fastsanger input --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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299 <param name="sc" value="false" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
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300 <param name="careful" value="false" /> |
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301 <param name="kmers" value="33" /> |
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302 <param name="lib_type" value="paired_end" /> |
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303 <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" /> |
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304 <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" /> |
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305 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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306 <output name="out_contig_stats"> |
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307 <assert_contents> |
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308 <has_text_matching expression="NODE_1\t1000"/> |
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309 </assert_contents> |
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310 </output> |
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311 </test> |
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312 <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input --> |
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313 <param name="sc" value="false" /> |
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314 <param name="careful" value="false" /> |
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315 <param name="kmers" value="33" /> |
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316 <param name="lib_type" value="paired_end" /> |
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317 <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" /> |
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318 <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" /> |
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319 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> |
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320 <output name="out_contig_stats"> |
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321 <assert_contents> |
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322 <has_text_matching expression="NODE_1\t1000"/> |
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323 </assert_contents> |
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324 </output> |
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325 </test> |
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326 </tests> |
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327 <help> |
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328 <![CDATA[ |
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329 **What it does** |
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330 |
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331 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. |
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332 |
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333 This wrapper runs SPAdes, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. |
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334 |
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335 **License** |
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336 |
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337 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. |
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338 |
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339 This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. |
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340 |
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341 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. |
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342 |
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343 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. |
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344 |
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345 ** Acknowledgments ** |
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346 |
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347 Original wrapper developed by Lionel Guy. |
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348 |
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349 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. |
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350 |
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351 Nicola Soranzo fixed various bugs. |
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352 |
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353 Simon Gladman added fastg optional outputs. |
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354 ]]> |
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355 </help> |
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356 <citations> |
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357 <citation type="doi">10.1089/cmb.2012.0021</citation> |
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358 </citations> |
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359 </tool> |