| Previous changeset 18:e7ee3aadf1a5 (2021-09-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538" |
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modified:
chira_extract.xml macros.xml |
| b |
| diff -r e7ee3aadf1a5 -r 73d2b7a8d94b chira_extract.xml --- a/chira_extract.xml Fri Sep 24 06:49:19 2021 +0000 +++ b/chira_extract.xml Sun Dec 19 15:47:37 2021 +0000 |
| [ |
| b'@@ -1,9 +1,9 @@\n-<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">\n+<tool id="chira_extract" name="ChiRA extract" version="@TOOL_VERSION@1">\n <description>extrat the chimeras</description>\n- <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements" />\n <command detect_errors="aggressive"><![CDATA[\n #set $genomic_fasta = \'\'\n@@ -17,16 +17,16 @@\n #end if\n #end if\n chira_extract.py\n- -l \'$loci\'\n+ --loci \'$loci\'\n #if str($annotation.annot_choice) == "yes":\n- -g \'$annotation.gtf\'\n+ --gtf \'$annotation.gtf\'\n #if $hybridize:\n- -f \'$genomic_fasta\'\n+ --ref \'$genomic_fasta\'\n #end if\n #end if\n- -tc \'$tpm_cutoff\'\n- -sc \'$score_cutoff\'\n- -co \'$chimeric_overlap\'\n+ --tpm_cutoff \'$tpm_cutoff\'\n+ --score_cutoff \'$score_cutoff\'\n+ --chimeric_overlap \'$chimeric_overlap\'\n #if str($reference.ref_type) == "single":\n -f1 \'$reference.ref_fasta\'\n #else if str($reference.ref_type) == "split":\n@@ -35,18 +35,19 @@\n #end if\n $hybridize\n $seed_interaction\n- -sbp \'$seed_bp\'\n- -smpu \'$seed_min_pu\'\n- -acc \'$accessibility\'\n- -accw \'$acc_width\'\n- -m \'$intarna_mode\'\n+ --seed_bp \'$seed_bp\'\n+ --seed_min_pu \'$seed_min_pu\'\n+ --accessibility \'$accessibility\'\n+ --acc_width \'$acc_width\'\n+ --intarna_mode \'$intarna_mode\'\n+ --temperature $temperature\n $summarize\n- -p "\\${GALAXY_SLOTS:-2}"\n- -o ./\n+ --processes "\\${GALAXY_SLOTS:-2}"\n+ --out ./\n ]]></command>\n \n <inputs>\n- <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>\n+ <param format="tabular" argument="--loci" type="data" label="File containing CRLs information"/>\n <conditional name="annotation">\n <param name="annot_choice" type="select" label="Have genomic information?"\n help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">\n@@ -54,19 +55,19 @@\n <option value="no">No</option>\n </param>\n <when value="yes">\n- <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>\n+ <param format="gtf,gff" argument="--gtf" type="data" label="Annotations in GTF format"/>\n <conditional name="fasta_source">\n <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">\n <option value="history" selected="true">History</option>\n <option value="preloaded">Server indexed files</option>\n </param>\n <when value="history">\n- <param name="fasta" type="data" format="fasta" label="Genomic FASTA file" />\n+ <param argument="--ref" name="fasta" type="data" format="fasta" label="Genomic FASTA file" />\n </when>\n <when value="preloaded">\n- <param name="fasta_id" type="select" label="Select FASTA index">\n- <options from_data_table="fasta_indexes" />\n- </param>\n+ <param argument="--ref" name="fasta_id" type="select" label="Select FASTA index">\n+ <options from_data_table="fasta_indexes" />\n+ </param>\n </when>\n </conditional>\n </when>\n@@ -74,11 +75,11 @@\n <!-- Do nothing -->\n </when>\n </conditional>\n- <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max='..b'nteger" value="2"\n+ <param argument="--chimeric_overlap" type="integer" value="2"\n label=" Maximum number of bases allowed between the chimericsegments of a read"/>\n <conditional name="reference">\n <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">\n@@ -86,40 +87,40 @@\n <option value="single">Single reference</option>\n </param>\n <when value="split">\n- <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"\n+ <param format="fasta" argument="--ref_fasta1" type="data" label="Reference FASTA file"\n help="Reference fasta file"/>\n- <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"\n+ <param format="fasta" argument="--ref_fasta2" type="data" label="Second reference FASTA file"\n help="Second reference fasta file."/>\n </when>\n <when value="single">\n- <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"\n+ <param format="fasta" argument="--ref_fasta1" name="ref_fasta" type="data" label="Reference FASTA file"\n help="Reference fasta file"/>\n </when>\n </conditional>\n- <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"\n+ <param argument="--hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"\n label="Hybridize chimeric loci?"\n help="Turning this option on increases the run time of the tool significantly."/>\n- <param name="intarna_mode" type="select">\n+ <param argument="--intarna_mode" type="select">\n <option value="H">Heuristic</option>\n <option value="M">Exact</option>\n <option value="S">Seed-only</option>\n </param>\n- <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true"\n+ <param argument="--no_seed" name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true"\n label="Enforce seed interaction?"/>\n- <param name="seed_bp" type="integer" value="5" min="2" max="20"\n+ <param argument="--seed_bp" type="integer" value="5" min="2" max="20"\n label="Number of inter-molecular base pairs within the seed region"\n help="IntaRNA --seedBP parameter"/>\n- <param name="seed_min_pu" type="float" value="0" min="0" max="1"\n+ <param argument="--seed_min_pu" type="float" value="0" min="0" max="1"\n label="Minimal unpaired probability (per sequence) a seed region may have"\n help="IntaRNA --seedMinPu parameter"/>\n- <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"\n+ <param argument="--accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"\n label="Compute accessibility profiles for interacting sequences?"/>\n- <param name="acc_width" type="integer" value="150" min="0" max="99999"\n+ <param argument="--acc_width" type="integer" value="150" min="0" max="99999"\n label="Sliding window size for accessibility computation"\n help="IntaRNA --accW parameter"/>\n- <param name="temperature" type="float" value="37" min="0" max="100"\n+ <param argument="--temperature" type="float" value="37" min="0" max="100"\n label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>\n- <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"\n+ <param argument="--summerize" name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"\n label="Summarize interactions at loci level?"/>\n </inputs>\n \n' |
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| diff -r e7ee3aadf1a5 -r 73d2b7a8d94b macros.xml --- a/macros.xml Fri Sep 24 06:49:19 2021 +0000 +++ b/macros.xml Sun Dec 19 15:47:37 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> + <token name="@TOOL_VERSION@">@TOOL_VERSION@+galaxy</token> <token name="@TOOL_VERSION@">1.4.3</token> <xml name="bio_tools"> <xrefs> |