| Previous changeset 0:23f5701549b1 (2011-09-12) Next changeset 2:cca0838c1597 (2013-02-26) |
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Commit message:
Add tool_dependencies and functional test |
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modified:
cd_hit_est.xml |
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added:
test-data/cd_hit_est_in.fa tool_dependencies.xml |
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| diff -r 23f5701549b1 -r 34a799d173f7 cd_hit_est.xml --- a/cd_hit_est.xml Mon Sep 12 10:43:08 2011 -0400 +++ b/cd_hit_est.xml Fri Sep 07 13:52:03 2012 -0500 |
| [ |
| @@ -1,5 +1,8 @@ -<tool id="cd_hit_est" name="CD-HIT-EST" version="1.0"> +<tool id="cd_hit_est" name="CD-HIT-EST" version="1.1"> <description>Cluster a nucleotide dataset into representative sequences</description> + <requirements> + <requirement type="package" version="4.6.1">cd-hit</requirement> + </requirements> <command> cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand </command> @@ -24,10 +27,23 @@ <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/> <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/> </outputs> - <requirements> - <requirement type="binary">cd-hit-est</requirement> - </requirements> <tests> + <test> + <param name="fasta_in" value="cd_hit_est_in.fa" /> + <param name="similarity" value="0.9"/> + <param name="wordsize" value="8"/> + <output name="clusters_out"> + <assert_contents> + <has_text text=">Cluster" /> + <has_text_matching expression=">F12Fcsw_481739" /> + </assert_contents> + </output> + <output name="fasta_out"> + <assert_contents> + <has_text_matching expression="^>[MF]\d\dFcsw_\d*" /> + </assert_contents> + </output> + </test> </tests> <help> **CD-HIT-EST** |
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| diff -r 23f5701549b1 -r 34a799d173f7 test-data/cd_hit_est_in.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd_hit_est_in.fa Fri Sep 07 13:52:03 2012 -0500 |
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| b'@@ -0,0 +1,74 @@\n+>F12Fcsw_481739\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGACGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F14Fcsw_133982\n+GGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGCCCAA\n+>F14Fcsw_149685\n+GGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F14Fcsw_175165\n+CGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F14Fcsw_176364\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGCCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACGCGGTCCAA\n+>F14Fcsw_224425\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTAAGACACGGTCCAA\n+>F14Fcsw_27361\n+CGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F14Fcsw_2745\n+GACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F14Fcsw_37069\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGCCCAG\n+>F14Fcsw_38031\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCAA\n+>F14Fcsw_49588\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACGCGGTCCAA\n+>F22Fcsw_400293\n+CCGGCGCACGGGTGAGTAACACGTATCCAACCTTCCGTACACTCAGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGGATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGGCAACGATCAGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F23Fcsw_133990\n+GGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCGACAACACTGGGATAGCCTTTCGAAAGAAAGATTAATACCGGATGGCATAGTTTTCCCGCATGGAAAAACTATTAAAGAATTTCGGTTATCGATGGGGATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F23Fcsw_160873\n+CGGGTGAGTAACGCGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGGTAGTAGGCGGGGTAACGGCCCACCTAGCCAACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F23Fcsw_86009\n+GGCGACCGGCGCACGGGTGAGTAACGCGTATCCAACCTTCCGTACACTCAGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGGATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGGCAACGATCAGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>F23Fcsw_96640\n+TCCGTACACTCAGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGAATTTCGGTCATCGATGGGGATGCGT'..b'GGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M13Fcsw_127764\n+GACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACGACGATGCGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAA\n+>M13Fcsw_128004\n+CGGACGGGTGAGTAACGCGTGAGTAACCTGCCGATAACTCAGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGAATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGGCGACGATGCGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAA\n+>M13Fcsw_198303\n+TAACACGTATCCAACCTGCCTCATACTCGGGGATAACCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTCAACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M14Fcsw_117325\n+GTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M14Fcsw_151062\n+CGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M14Fcsw_181677\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M14Fcsw_186607\n+GACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGGTTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGCGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M24Fcsw_136217\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTCTGATTAGCTTGTTGGCGGGGTAACGGCCCACCAAGGCACCGATCAGTAGGGGTTCTGAGAGGAAGGTCCCCCACATAGGAACTGAGACACGGTCCTA\n+>M41Fcsw_259146\n+ACCGGCGCACGGGTGAGTAACACGTATCCAACCTACCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGCCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M42Fcsw_137216\n+CAACCTACCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M42Fcsw_138199\n+GACCGGCGCACGGGTGAGTAACACGTATCCAACCTACCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M42Fcsw_225418\n+CACGTATCCAACCTGCCGTCTACTCTTGGACAGCCTTCTGAAAGGAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGGATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGCCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCACATTGGAACTGAGACACGGTCCAA\n+>M42Fcsw_263016\n+ACCTACCTCATACTCGGGGATAGCCTTTCGAAAGAAAGATTAATATCCGATAGCATATATTTCCCGCATGGGTTTTATATTAAAGAAATTCGGTATGAGATGGGGATGCGTTCCATTAGTTTGTTGGGGGGTAACGGCCCACCAAGACTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCCA\n+>M42Fcsw_334979\n+GGGATAGCCGCCCGAAAGGACGGGTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGGATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCAAGCCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M43Fcsw_250770\n+GTATCCAACCTGCCGTCTACTCTTGGACAGCCTTCTGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGGATTTCGGTCATCGATGGGGATGCGTTCCATTAGGTTGTTGGCGGGGTAACGGCCCACCTAGTCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n+>M44Fcsw_200453\n+CTAGTGGCGGACGGGTGAGTAACGCGTATCCAACCTGCCGATGACTCGGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGCATAGTTCTTCCGCATGGTAGAACTATTAAAGAACTTCGGTCATCGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAA\n' 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| diff -r 23f5701549b1 -r 34a799d173f7 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 07 13:52:03 2012 -0500 |
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| @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cd-hit" version="4.6.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz</action> + <action type="shell_command">make openmp=yes</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the cdhit package: + +http://weizhong-lab.ucsd.edu/cd-hit/ + +https://code.google.com/p/cdhit/ + +https://code.google.com/p/cdhit/source/browse/README + + </readme> + </package> +</tool_dependency> + |