srnapipe: sRNAPipe.xml annotate

annotate sRNAPipe.xml @ 66:ff36e76d696a draft

planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 42877e3bba93278af4319cee455e189712cc85c3

author	brasset_jensen
date	Wed, 30 Jan 2019 06:26:32 -0500
parents	0e9adbd82bb4
children	740884893563

rev	line source
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	2 <description>In-depth study of small RNA</description>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	3 <macros>
62 e6c4f3e96e47 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 87e0c95b4d0d1954e81247c31a8f74c5d87c7f9e pierre.pouchin parents: 61 diff changeset	4 <xml name="source" token_arg="Argument" token_build="Build argument">
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	5 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	6 <param name="source" type="select" label="Will you select the database from your history or use a built-in index?">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	7 <option value="indexed">Use a built-in index</option>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	8 <option value="history">Use one from the history</option>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	9 </param>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	10 <when value="indexed">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	11 <param name="indices" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	12 <options from_data_table="bwa_indexes">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	13 <filter type="sort_by" column="2" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	14 <validator type="no_options" message="No indexes are available" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	15 </options>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	16 </param>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	17 </when>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	18 <when value="history">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	19 <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	20 </when>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	21 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	22 </xml>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	23 </macros>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	24 <requirements>
65 0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	25 <requirement type="package" version="1.9">samtools</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	26 <requirement type="package">bwa</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	27 <requirement type="package">bedtools</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	28 <requirement type="package">perl</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	29 <requirement type="package">perl-getopt-long</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	30 <requirement type="package">perl-parallel-forkmanager</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	31 <requirement type="package">perl-statistics-r</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	32 <requirement type="package">perl-string-random</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	33 <requirement type="package">perl-file-copy-recursive</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	34 <requirement type="package">perl-math-cdf</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	35 <requirement type="package">r-base</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	36 <requirement type="package">r-plotrix</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	37 <requirement type="package">r-rcolorbrewer</requirement>
0e9adbd82bb4 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a623ac00600191204ede63c45862a7fbb561afd2 brasset_jensen parents: 64 diff changeset	38 <requirement type="package">r-ggplot2</requirement>
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	39 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	40 </requirements>
64 967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d brasset_jensen parents: 63 diff changeset	41 <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl' \| grep 'version' \| grep "version" \| cut -d ' ' -f 3</version_command>
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	42 <command detect_errors="aggressive"><![CDATA[
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	43 perl '$__tool_directory__/bin/sRNAPipe.pl'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	44
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	45 --fastq '${first_input}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	46 --fastq_n '${first_input.name}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	47 #for $input_file in $input_files:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	48 --fastq '${input_file.additional_input}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	49 --fastq_n '${input_file.additional_input.name}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	50 #end for
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	51
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	52 #if $genome.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	53 --ref '${genome.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	54 --build_index
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	55 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	56 --ref '${genome.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	57 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	58
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	59 #if $tRNAs.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	60 --tRNAs '${tRNAs.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	61 --build_tRNAs
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	62 #elif $tRNAs.source.source == "none":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	63 --tRNAs "None"
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	64 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	65 --tRNAs '${tRNAs.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	66 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	67
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	68 #if $snRNAs.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	69 --snRNAs '${snRNAs.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	70 --build_snRNAs
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	71 #elif $snRNAs.source.source == "none":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	72 --snRNAs "None"
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	73 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	74 --snRNAs '${snRNAs.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	75 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	76
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	77 #if $rRNAs.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	78 --rRNAs '${rRNAs.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	79 --build_rRNAs
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	80 #elif $rRNAs.source.source == "none":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	81 --rRNAs "None"
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	82 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	83 --rRNAs '${rRNAs.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	84 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	85
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	86 #if $miRNAs.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	87 --miRNAs '${miRNAs.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	88 --build_miRNAs
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	89 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	90 --miRNAs '${miRNAs.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	91 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	92
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	93 #if $transcripts.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	94 --transcripts '${transcripts.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	95 --build_transcripts
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	96 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	97 --transcripts '${transcripts.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	98 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	99
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	100 #if $TE.source.source == "history":
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	101 --TE '${TE.source.file}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	102 --build_TE
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	103 #else:
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	104 --TE '${TE.source.indices.fields.path}'
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	105 #end if
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	106
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	107 --si_min $si_min
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	108 --si_max $si_max
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	109 --pi_min $pi_min
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	110 --pi_max $pi_max
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	111 --min $min
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	112 --max $max
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	113
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	114 --mis $mis
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	115 --misTE $misTE
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	116 --dir $html_out.files_path
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	117 --html $html_out
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	118 --PPPon $PPPon
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	119 ]]>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	120 </command>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	121
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	122 <inputs>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	123 <param name="first_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name with --fastq_n"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	124 <repeat name="input_files" title="Additional Fastq Files">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	125 <param name="additional_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name after each fastq with --fastq_n"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	126 </repeat>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	127 <section name="genome" title="Reference genome" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	128 <expand macro="source" arg="--ref" build="--build_index"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	129 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	130 <section name="transcripts" title="Transcripts" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	131 <expand macro="source" arg="--transcripts" build="--build_transcripts"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	132 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	133 <section name="TE" title="Transposable Elements" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	134 <expand macro="source" arg="--TE" build="--build_TE"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	135 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	136 <section name="miRNAs" title="miRNAs" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	137 <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	138 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	139 <section name="snRNAs" title="snRNAs" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	140 <expand macro="source" arg="--snRNAs" build="--build_snRNAs"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	141 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	142 <section name="rRNAs" title="rRNAs" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	143 <expand macro="source" arg="--rRNAs" build="--build_rRNAs"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	144 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	145 <section name="tRNAs" title="tRNAs" expanded="true">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	146 <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	147 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	148
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	149 <param name="min" argument="--min" type="integer" value="18" label="minimum read size"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	150 <param name="max" argument="--max" type="integer" value="29" label="maximum read size"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	151 <param name="si_min" argument="--si_min" type="integer" value="21" label="lower bound of siRNA range"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	152 <param name="si_max" argument="--si_max" type="integer" value="21" label="higher bound of siRNA range"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	153 <param name="pi_min" argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	154 <param name="pi_max" argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	155 <param name="mis" argument="--mis" type="integer" value="0" label="maximal genome mismatches"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	156 <param name="misTE" argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	157 <param name="PPPon" argument="--PPPon" type="boolean" checked="true" label="PPPartners"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	158 </inputs>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	159 <outputs>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	160 <data format="html" name="html_out" label="${tool.name} on ${first_input.name} (${on_string}): HTML report"/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	161 <collection type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	162 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	163 </collection>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	164 </outputs>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	165 <tests>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	166 <test>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	167 <param name="first_input" value="reads-sample-small.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	168 <section name="genome">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	169 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	170 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	171 <param name="file" value ="genome-small.fa" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	172 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	173 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	174 <section name="transcripts">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	175 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	176 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	177 <param name="file" value ="transcripts-file-small.fa" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	178 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	179 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	180 <section name="TE">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	181 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	182 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	183 <param name="file" value ="TE-file-small.fa" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	184 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	185 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	186 <section name="miRNAs">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	187 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	188 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	189 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	190 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	191 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	192 <section name="snRNAs">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	193 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	194 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	195 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	196 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	197 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	198 <section name="rRNAs">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	199 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	200 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	201 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	202 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	203 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	204 <section name="tRNAs">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	205 <conditional name="source">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	206 <param name="source" value="history" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	207 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	208 </conditional>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	209 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	210 <param name="min" value="18" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	211 <param name="max" value="29" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	212 <param name="si_min" value="21" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	213 <param name="si_max" value="21" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	214 <param name="pi_min" value="23" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	215 <param name="pi_max" value="29" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	216 <param name="mis" value="0" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	217 <param name="misTE" value="3" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	218 <param name="PPPon" value="true" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	219 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	220 <output_collection name="output_fastqsanger" type="list">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	221 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	222 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	223 <element name="reads-sample-small.fastq-bonafide_reads-genome_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	224 <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	225 <element name="reads-sample-small.fastq-bonafide_reads-TEs_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	226 <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	227 <element name="reads-sample-small.fastq-bonafide_reads-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	228 <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	229 <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	230 <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	231 <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	232 <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	233 <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	234 <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	235 <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	236 <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	237 <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	238 <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	239 <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	240 <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	241 <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	242 <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	243 <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	244 <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	245 <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	246 <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	247 </output_collection>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	248 </test>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	249 </tests>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	250 <help>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	251 User manual
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	252 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	253 </help>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	254 <citations>
66 ff36e76d696a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 42877e3bba93278af4319cee455e189712cc85c3 brasset_jensen parents: 65 diff changeset	255 <citation type="doi">10.1186/s13100-018-0130-7</citation>
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	256 </citations>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	257 </tool>

Mercurial > repos > brasset_jensen > srnapipe

annotate sRNAPipe.xml @ 66:ff36e76d696a draft