Mercurial > repos > iuc > meme_fimo
diff fimo.xml @ 10:307b2f3559bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2017 20:39:58 -0400 |
| parents | 53846f74a019 |
| children | c470b36b592d |
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--- a/fimo.xml Mon Nov 14 13:17:22 2016 -0500 +++ b/fimo.xml Thu Jun 29 20:39:58 2017 -0400 @@ -1,66 +1,57 @@ -<tool id="meme_fimo" name="FIMO" version="4.11.1.0"> +<tool id="meme_fimo" name="FIMO" version="4.11.2.0"> <description>- Scan a set of sequences for motifs.</description> - <requirements> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> - <requirement type="package" version="4.11.1">meme</requirement> - </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> - <![CDATA[ - mkdir -p output && - python $__tool_directory__/fimo_wrapper.py - --input_motifs "${input_motifs}" - #if str($fasta_type.fasta_type_selector) == 'history': - --input_fasta "${fasta_type.input_database}" - #else: - --input_fasta "${fasta_type.input_database.fields.path}" - #end if - --options_type $options_type.options_type_selector - #if str($options_type.options_type_selector) == 'advanced': - --alpha "${options_type.alpha}" - #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': - --bgfile "motif-file" - #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': - --bgfile "${options_type.bgfile_type.bgfile}" - #end if - ${options_type.max_strand} - --max_stored_scores "${options_type.max_stored_scores}" - #if str($options_type.motifs_cond.motifs_selector) == 'no': - #for $motif in $options_type.motifs: - --motif "${motif.motif}" - #end for - #end if - --output_separate_motifs ${options_type.output_separate_motifs} - --motif_pseudo "${options_type.motif_pseudo}" - ${options_type.no_qvalue} - ${options_type.norc} - #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': - --parse_genomic_coord 'yes' - --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} - #end if - #if str($options_type.psp_cond.psp_selector) == 'yes': - --input_psp "${input_psp}" - #end if - #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': - --input_prior_dist "${input_prior_dist}" - #end if - ${options_type.qv_thresh} - --thresh ${options_type.thresh} - #end if - --output_path '${html_outfile.files_path}' - --html_output "${html_outfile}" - --interval_output '${interval_outfile}' - --txt_output "${txt_outfile}" - --xml_output "${xml_outfile}" - --gff_output "${gff_outfile}" - ]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +mkdir -p output && +python '$__tool_directory__/fimo_wrapper.py' +--input_motifs '${input_motifs}' +#if str($fasta_type.fasta_type_selector) == 'history': + --input_fasta '${fasta_type.input_database}' +#else: + --input_fasta '${fasta_type.input_database.fields.path}' +#end if +--options_type $options_type.options_type_selector +#if str($options_type.options_type_selector) == 'advanced': + --alpha '${options_type.alpha}' + #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': + --bgfile 'motif-file' + #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': + --bgfile '${options_type.bgfile_type.bgfile}' + #end if + ${options_type.max_strand} + --max_stored_scores '${options_type.max_stored_scores}' + #if str($options_type.motifs_cond.motifs_selector) == 'no': + #for $motif in $options_type.motifs: + --motif '${motif.motif}' + #end for + #end if + --output_separate_motifs ${options_type.output_separate_motifs} + --motif_pseudo '${options_type.motif_pseudo}' + ${options_type.no_qvalue} + ${options_type.norc} + #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': + --parse_genomic_coord 'yes' + --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} + #end if + #if str($options_type.psp_cond.psp_selector) == 'yes': + --input_psp '${input_psp}' + #end if + #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': + --input_prior_dist '${input_prior_dist}' + #end if + ${options_type.qv_thresh} + --thresh ${options_type.thresh} +#end if +--output_path '${html_outfile.files_path}' +--html_output '${html_outfile}' +--interval_output '${interval_outfile}' +--txt_output '${txt_outfile}' +--xml_output '${xml_outfile}' +--gff_output '${gff_outfile}' + ]]></command> <inputs> <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/> <conditional name="fasta_type">