Mercurial > repos > crusoe > khmer
changeset 11:cec78b574760
Actually import the macros
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 09:47:37 -0400 |
| parents | d00e18a0a3f2 |
| children | 760990dd7983 |
| files | abundance-dist-single.xml abundance-dist.xml count-median.xml filter-abund.xml macros.xml normalize-by-median.xml |
| diffstat | 6 files changed, 37 insertions(+), 61 deletions(-) [+] |
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--- a/abundance-dist-single.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/abundance-dist-single.xml Sun Jun 29 09:47:37 2014 -0400 @@ -9,6 +9,7 @@ </description> <macros> <token name="@BINARY@">abundance-dist-single.py</token> + <import>macros.xml</import> </macros> <expand macro="requirements" /> <command>
--- a/abundance-dist.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/abundance-dist.xml Sun Jun 29 09:47:37 2014 -0400 @@ -1,5 +1,5 @@ <tool id="gedlab-khmer-normalize-by-median" - name="Abundance Dist" + name="Abundance Distribution" version="1.1-1" force_history_refresh="true"> @@ -8,7 +8,8 @@ file using a pre-made k-mer counting table. </description> <macros> - <token name="@BINARY@">abundance-dist-single.py</token> + <token name="@BINARY@">abundance-dist-single.py</token> + <import>macros.xml</import> </macros> <expand macro="requirements" /> <command>
--- a/count-median.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/count-median.xml Sun Jun 29 09:47:37 2014 -0400 @@ -9,7 +9,8 @@ estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). </description> <macros> - <token name="@BINARY@">count-median.py</token> + <token name="@BINARY@">count-median.py</token> + <import>macros.xml</import> </macros> <expand macro="requirements" /> <command>
--- a/filter-abund.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/filter-abund.xml Sun Jun 29 09:47:37 2014 -0400 @@ -7,37 +7,23 @@ Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer counting table. </description> - - <requirements> - <requirement - type="package" - version="1.1"> - khmer - </requirement> - </requirements> - - <version_command> - filter-abund.py --version - </version_command> - + <macros> + <token name="@BINARY@">filter-abund.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command> mkdir output; cd output; filter-abund.py $variable_coverage - $presencetable_to_load + $countingtable_to_load #for input in $inputs $input #end for </command> <inputs> - <param name="inputs" - multiple="true" - type="data" - format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" - label="FAST[AQ] file(s)" - help="Put in order of precedence such as longest reads first." /> - + <expand macro="multifile-fastaq-inputs" /> <param name="variable_coverage" type="boolean" checked="false" @@ -45,19 +31,10 @@ falsevalue="" label="Variable coverage" help="Only trim when a sequence has high enough coverage (median abundance > 20)" /> - - <param name="presencetable_to_load" - type="data" - optional="false" - label="the khmer abundance table to load" - help="The inputs file(s) will be processed using the kmer counts in the specified k-mer counting table file." /> + <expand macro="input_counting_table_filename" /> </inputs> <outputs> - <data name="output" - format="input" - label="${tool.name} processed nucleotide sequence file"> - <discover_datasets pattern="__name__" directory="output" visible="true"/> - </data> + <expand macro="output_sequences" /> </outputs> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
--- a/macros.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/macros.xml Sun Jun 29 09:47:37 2014 -0400 @@ -68,6 +68,14 @@ </when> </conditional> </xml> + <xml name="input_sequences_filenames"> + <param name="inputs" + multiple="true" + type="data" + format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" + label="FAST[AQ] file(s)" + help="Put in order of precedence such as longest reads first." /> + </xml> <xml name="input_sequence_filename"> <param name="input_sequence_filename" type="data" @@ -89,4 +97,11 @@ k-mers."> </data> </xml> + <xml name="output_sequences"> + <data name="output" + format="input" + label="${tool.name} processed nucleotide sequence file"> + <discover_datasets pattern="__name__" directory="output" visible="true"/> + </data> + </xml> </macros>
--- a/normalize-by-median.xml Sun Jun 29 09:22:32 2014 -0400 +++ b/normalize-by-median.xml Sun Jun 29 09:47:37 2014 -0400 @@ -7,19 +7,11 @@ Filters a fastq/fasta file using digital normalization via median k-mer abundances. </description> - - <requirements> - <requirement - type="package" - version="1.1"> - khmer - </requirement> - </requirements> - - <version_command> - normalize-by-median.py --version - </version_command> - + <macros> + <token name="@BINARY@">normalize-by-median.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command> mkdir output; cd output; @@ -48,13 +40,7 @@ </command> <inputs> - <param name="inputs" - multiple="true" - type="data" - format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" - label="FAST[AQ] file(s)" - help="Put in order of precedence such as longest reads first." /> - + <expand macro="input_sequences_filenames" /> <param name="paired_switch" type="boolean" checked="false" @@ -137,12 +123,7 @@ label="${tool.name} k-mer counting table from #echo ', '.join(map(str, $inputs ))#"> <filter>save_countingtable == True</filter> </data> - <data name="outputs" - format="input" - label="${tool.name} processed nucleotide sequence file"> - <discover_datasets pattern="__name__" directory="output" visible="true"/> - </data> - + <expand macro="output_sequences" /> </outputs> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->