Adding support for the remaining parameters

build.xml

@@ -6,7 +6,7 @@
 <target name="create-zip" depends="init">
     <antcall target="prezip"/>
     <zip destfile="${dest.dir}/${ant.project.name}.zip" whenempty="fail" defaultexcludes="true">
-        <fileset dir="." includes="manifest, doc.html, Dockerfile, LICENSE"/>
+        <fileset dir="." includes="manifest, doc.html, Dockerfile, LICENSE, paramgroups.json"/>
         <zipfileset dir="src" includes="call_kallisto.sh, transcript2genes.R"/>
     </zip>
     <antcall target="postzip"/>

manifest

@@ -4,12 +4,14 @@ JVMLevel=
 LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00383\:2
 author=Edwin F. Juarez;GenePattern -- Mesirov Lab
 categories=rna-seq
-commandLine=/module/call_kallisto.sh <fastq_files> <transcriptome> <output_filename> <extra_commands>
+commandLine=/module/call_kallisto.sh <fastq_files> <transcriptome> <bias> <output_filename> <bootstrap_samples> <seed> \
+    <quantify_reads> <include_overhang> <read_direction> fl_<fragment_length> fsd_<fragment_sd> <pseudobam> <genomebam> \
+    gtf_<gtf_file> chr_<chromosome_file>
 cpuType=any
-description=Running Kallisto with basic or custom parameters to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation.
+description=Runs Kallisto to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation
 fileFormat=csv
 
-job.docker.image=genepattern/kallisto\:5.46.1
+job.docker.image=genepattern/kallisto\:6
 job.memory=4Gb
 language=any
 name=Kallisto
@@ -45,37 +47,187 @@ p2_value=Human\=Human (Gencode v37 -- GRCh38.p13);Mouse\=Mouse (Gencode M26 -- G
 
 p3_MODE=
 p3_TYPE=TEXT
-p3_default_value=expression_data
-p3_description=Provide the base name of the files to be created.
+p3_default_value=NO
+p3_description=Perform sequence based bias correction
 p3_fileFormat=
 p3_flag=
-p3_name=output_filename
+p3_name=bias
 p3_numValues=0..1
 p3_optional=
 p3_prefix=
 p3_prefix_when_specified=
 p3_type=java.lang.String
-p3_value=
+p3_value=NO\=NO;YES\=YES
 
 p4_MODE=
 p4_TYPE=TEXT
-p4_default_value=
-p4_description=Write here what other parameters you want to pass to Kallisto, e.g., for single-end data, you can write "--single --fragment-length\=200 --sd\=30"
+p4_default_value=expression_data
+p4_description=Provide the base name of the files to be created.
 p4_fileFormat=
 p4_flag=
-p4_name=extra_commands
+p4_name=output_filename
 p4_numValues=0..1
-p4_optional=on
+p4_optional=
 p4_prefix=
 p4_prefix_when_specified=
 p4_type=java.lang.String
 p4_value=
 
+p5_MODE=
+p5_default_value=2
+p5_description=Number of bootstrap samples
+p5_fileFormat=
+p5_flag=
+p5_name=bootstrap_samples
+p5_numValues=0..1
+p5_optional=
+p5_prefix=
+p5_prefix_when_specified=
+p5_type=java.lang.Integer
+p5_value=
+
+p6_MODE=
+p6_default_value=42
+p6_description=Seed for the bootstrap sampling
+p6_fileFormat=
+p6_flag=
+p6_name=seed
+p6_numValues=0..1
+p6_optional=
+p6_prefix=
+p6_prefix_when_specified=
+p6_type=java.lang.Integer
+p6_value=
+
+p7_MODE=
+p7_TYPE=TEXT
+p7_default_value=NO
+p7_description=Quantify single-end reads
+p7_fileFormat=
+p7_flag=
+p7_name=quantify_reads
+p7_numValues=0..1
+p7_optional=
+p7_prefix=
+p7_prefix_when_specified=
+p7_type=java.lang.String
+p7_value=NO\=NO;YES\=YES
+
+p8_MODE=
+p8_TYPE=TEXT
+p8_default_value=NO
+p8_description=Include reads where unobserved rest of fragment is predicted to lie outside a transcript
+p8_fileFormat=
+p8_flag=
+p8_name=include_overhang
+p8_numValues=0..1
+p8_optional=
+p8_prefix=
+p8_prefix_when_specified=
+p8_type=java.lang.String
+p8_value=NO\=NO;YES\=YES
+
+p9_MODE=
+p9_TYPE=TEXT
+p9_default_value=not set
+p9_description=For strand specific reads, first read forward, first read reverse or unspecified
+p9_fileFormat=
+p9_flag=
+p9_name=read_direction
+p9_numValues=0..1
+p9_optional=
+p9_prefix=
+p9_prefix_when_specified=
+p9_type=java.lang.String
+p9_value=notset\=not set;forward\=first read forward;reverse\=first read reverse
+
+p10_MODE=
+p10_default_value=
+p10_description=Estimated average fragment length (float value)
+p10_fileFormat=
+p10_flag=
+p10_name=fragment_length
+p10_numValues=0..1
+p10_optional=on
+p10_prefix=
+p10_prefix_when_specified=
+p10_type=java.lang.Float
+p10_value=
+
+p11_MODE=
+p11_default_value=
+p11_description=Estimated standard deviation of fragment length; values are estimated with paired end data, but are required when using single-end reads (float value)
+p11_fileFormat=
+p11_flag=
+p11_name=fragment_sd
+p11_numValues=0..1
+p11_optional=on
+p11_prefix=
+p11_prefix_when_specified=
+p11_type=java.lang.Float
+p11_value=
+
+p12_MODE=
+p12_TYPE=TEXT
+p12_default_value=NO
+p12_description=Save pseudoalignments to transcriptome to BAM file
+p12_fileFormat=
+p12_flag=
+p12_name=pseudobam
+p12_numValues=0..1
+p12_optional=
+p12_prefix=
+p12_prefix_when_specified=
+p12_type=java.lang.String
+p12_value=NO\=NO;YES\=YES
+
+p13_MODE=
+p13_TYPE=TEXT
+p13_default_value=NO
+p13_description=Project pseudoalignments to genome sorted BAM file
+p13_fileFormat=
+p13_flag=
+p13_name=genomebam
+p13_numValues=0..1
+p13_optional=
+p13_prefix=
+p13_prefix_when_specified=
+p13_type=java.lang.String
+p13_value=NO\=NO;YES\=YES
+
+p14_MODE=IN
+p14_TYPE=FILE
+p14_default_value=
+p14_description=GTF file for transcriptome information, required for projecting pseudoalignments to genome sorted BAM file
+p14_fileFormat=gtf
+p14_flag=
+p14_name=gtf_file
+p14_numValues=0..1
+p14_optional=on
+p14_prefix=
+p14_prefix_when_specified=
+p14_type=java.io.File
+p14_value=
+
+p15_MODE=IN
+p15_TYPE=FILE
+p15_default_value=
+p15_description=Tab separated file with chromosome names and lengths, optional for projecting pseudoalignments to genome sorted BAM file, but recommended
+p15_fileFormat=tsv;csv
+p15_flag=
+p15_name=chromosome_file
+p15_numValues=0..1
+p15_optional=on
+p15_prefix=
+p15_prefix_when_specified=
+p15_type=java.io.File
+p15_value=
+
 privacy=public
 publicationDate=09/13/2019 19\:05 
 quality=production
 src.repo=https://github.com/genepattern/Kallisto/releases/tag/v2
 taskDoc=doc.html
 taskType=rna-seq
 userid=edjuaro
-version=Added Mouse index, Release M26 (GRCm39), and updated Human index, Release 37 (GRCh38.p13), from Gencode.
+version=Exposing all Kallisto parameters

paramgroups.json

@@ -0,0 +1,39 @@
+[
+  { name: "Basic Parameters",
+    parameters: [ 
+      "fastq_files",
+      "transcriptome",
+      "bias",
+      "output_filename"
+    ]
+  },
+  { name: "Bootstrapping Parameters",
+    description: "These parameters configure bootstrap sampling",
+    hidden: true,
+    parameters: [
+      "bootstrap_samples",
+      "seed"
+    ]
+  },
+  { name: "Single End Read Parameters",
+    description: "These parameters are only used with single-end reads",
+    hidden: true,
+    parameters: [
+      "quantify_reads",
+      "include_overhang",
+      "read_direction",
+      "fragment_length",
+      "fragment_sd"
+    ]
+  },
+  { name: "BAM Parameters",
+    description: "These parameters are used when savings alignments to a BAM file",
+    hidden: true,
+    parameters: [
+      "pseudobam",
+      "genomebam",
+      "gtf_file",
+      "chromosome_file"
+    ]
+  }
+]