annotate monorail.xml @ 8:0de07638de49 draft

Uploaded
author chrisw
date Wed, 13 Feb 2019 15:29:49 -0500
parents 03be34974b83
children 05932011f686
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
1 <tool id="monorail" name="Run the Monorail RNA-seq analysis pipeline" version="0.1.0">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
2 <requirements>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
3 <requirement type="package" version="1.9">samtools</requirement>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
4 <requirement type="package" version="2.6.0b">star</requirement>
5
d2d9937d1f9c Uploaded
chrisw
parents: 3
diff changeset
5 <requirement type="package" version="0.2.6">bamcount</requirement>
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
6 <requirement type="package" version="5.4.0">snakemake</requirement>
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
7 <requirement type="package" version="1.3.8">zstd</requirement>
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
8 </requirements>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
9 <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
11 snakemake --snakefile "$__tool_directory__/Snakefile
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
12 -j \${GALAXY_SLOTS:-4}
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
13 --config
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
14 #if str($singlePaired.sPaired) == "paired_collection"
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
15 inputs="$singlePaired.input.forward,$singlePaired.input.reverse"
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
16 #else
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
17 inputs="$singlePaired.input1"
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
18 #if str($singlePaired.sPaired) == "paired"
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
19 inputs="$singlePaired.input1,$singlePaired.input2"
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
20 #end if
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
21 #end if
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
22 output="./"
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
23 temp="./tmp"
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
24 ref="$refGenomeSource.GTFconditional.genomeDir.fields.path"
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
25 genome="ath10"
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
26 exon_bed="$exons"
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
27 study="SRP182756"
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
28 ]]></command>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
29 <inputs>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
30 <!-- FASTQ input(s) and options specifically for paired-end data. -->
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
31 <conditional name="singlePaired">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
32 <param name="sPaired" type="select" label="Single-end or paired-end reads">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
33 <option value="single" selected="true">Single-end</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
34 <option value="paired">Paired-end (as individual datasets)</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
35 <option value="paired_collection">Paired-end (as collection)</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
36 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
37 <when value="single">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
38 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
39 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
40 <when value="paired">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
41 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
42 <param format="fastq,fastq.gz" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
43 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
44 <when value="paired_collection">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
45 <param format="fastq,fastq.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
46 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
47 </conditional>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
48
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
49 <!--
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
50 <param name="refGenomeSource" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
51 <options from_data_table="rnastar_index2">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
52 <filter type="static_value" column="4" value="0"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
53 <filter type="sort_by" column="2" />
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
54 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
55 </options>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
56 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
57 -->
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
58
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
59 <!-- Genome source. -->
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
60 <conditional name="refGenomeSource">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
61 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
62 <option value="indexed" selected="True">Use a built-in index</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
63 <option value="history">Use reference genome from history and create temporary index</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
64 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
65 <when value="indexed">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
66 <conditional name="GTFconditional">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
67 <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
68 <option value="without-gtf">use genome reference without builtin gene-model</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
69 <option value="with-gtf">use genome reference with builtin gene-model</option>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
70 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
71 <when value="with-gtf">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
72 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
73 <options from_data_table="rnastar_index2">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
74 <filter type="static_value" column="4" value="1"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
75 <filter type="sort_by" column="2" />
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
76 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
77 </options>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
78 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
79 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
80 <when value="without-gtf">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
81 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
82 <options from_data_table="rnastar_index2">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
83 <filter type="static_value" column="4" value="0"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
84 <filter type="sort_by" column="2" />
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
85 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
86 </options>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
87 </param>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
88 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
89 </conditional>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
90 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
91 <when value="history">
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
92 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
93 </when>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
94 </conditional>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
95 <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
96 <param name="min_uniq_qual" type="integer" value="10" label="Minimum mapping quality for unique alignments" help="Set this to an appropriate integer value to filter out non-unique alignments"/>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
97 </inputs>
8
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
98 <outputs>
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
99 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>
0de07638de49 Uploaded
chrisw
parents: 7
diff changeset
100 <!--
6
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
101 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
7
03be34974b83 Uploaded
chrisw
parents: 6
diff changeset
102 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bc.auc.tsv"/>
03be34974b83 Uploaded
chrisw
parents: 6
diff changeset
103 <data format="txt" name="bc_log" label="${tool.name} on ${on_string}: bamcount log" from_work_dir="bc.log"/>
6
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
104 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"/>
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
105 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"/>
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
106 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam"/>
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
107 <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai"/>
4104eb494bf8 Uploaded
chrisw
parents: 5
diff changeset
108 -->
1
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
109 </outputs>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
110 <help>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
111 Run the Monorail RNA-seq analysis pipeline
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
112 </help>
5c92c1163a6d Uploaded
chrisw
parents:
diff changeset
113 </tool>