| Previous changeset 1:61718851f199 (2015-02-05) Next changeset 3:bc7d99f46a5d (2017-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744 |
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modified:
macros.xml seqtk_comp.xml seqtk_cutN.xml seqtk_dropse.xml seqtk_fqchk.xml seqtk_hety.xml seqtk_listhet.xml seqtk_mergefa.xml seqtk_mergepe.xml seqtk_mutfa.xml seqtk_randbase.xml seqtk_sample.xml seqtk_seq.xml seqtk_subseq.xml seqtk_trimfq.xml |
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| diff -r 61718851f199 -r f73729b62b51 macros.xml --- a/macros.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/macros.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -30,4 +30,8 @@ <https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute ]]> </token> + <xml name="citation"> + <citations> + </citations> + </xml> </macros> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_comp.xml --- a/seqtk_comp.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_comp.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -49,4 +49,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_cutN.xml --- a/seqtk_cutN.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_cutN.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -48,5 +48,6 @@ @ATTRIBUTION@ - ]]></help> +]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_dropse.xml --- a/seqtk_dropse.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_dropse.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -72,5 +72,6 @@ @ATTRIBUTION@ - ]]></help> +]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_fqchk.xml --- a/seqtk_fqchk.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_fqchk.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -55,4 +55,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_hety.xml --- a/seqtk_hety.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_hety.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -70,4 +70,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_listhet.xml --- a/seqtk_listhet.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_listhet.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -44,4 +44,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_mergefa.xml --- a/seqtk_mergefa.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_mergefa.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -65,4 +65,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_mergepe.xml --- a/seqtk_mergepe.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_mergepe.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -90,4 +90,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_mutfa.xml --- a/seqtk_mutfa.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_mutfa.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -48,4 +48,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_randbase.xml --- a/seqtk_randbase.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_randbase.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -42,4 +42,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_sample.xml --- a/seqtk_sample.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_sample.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -13,7 +13,7 @@ <inputs> <expand macro="in_faq" /> <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/> - <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/> + <param label="Subsample (decimal fraction or number)" name="subsample_size" type="float" value="100"/> </inputs> <outputs> <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/> @@ -35,4 +35,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_seq.xml --- a/seqtk_seq.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_seq.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -26,7 +26,9 @@ $N $x1 $x2 -$V +#if $in_file.ext == "fastqillumina" + -V +#end if $in_file > $default]]></command> @@ -48,7 +50,6 @@ <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/> <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/> <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/> - <param checked="false" label="shift quality by '(-Q) - 33' " help="(-V)" name="V" type="boolean" falsevalue="" truevalue="-V"/> </inputs> <outputs> <data format_source="in_file" hidden="false" name="default"/> @@ -73,4 +74,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_subseq.xml --- a/seqtk_subseq.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_subseq.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -80,4 +80,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |
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| diff -r 61718851f199 -r f73729b62b51 seqtk_trimfq.xml --- a/seqtk_trimfq.xml Thu Feb 05 12:00:43 2015 -0500 +++ b/seqtk_trimfq.xml Fri Jan 01 14:49:42 2016 -0500 |
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| @@ -59,4 +59,5 @@ @ATTRIBUTION@ ]]></help> + <expand macro="citation" /> </tool> |