view velocyto_cli.xml @ 1:883c33ef3372 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9

<tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy1">
    <description>pre-process data for the analysis of RNA velocity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam"/>
    <expand macro="requirements"/>
    <stdio>
      <!-- Anything other than zero is an error -->
      <exit_code level="fatal" range="1:"/>
      <exit_code level="fatal" range=":-1"/>
      <!-- In case the return code has not been set propery check stderr too -->
      <regex level="fatal" match="Error:" source="both" />
      <regex level="fatal" match="Exception:" source="both" />
      <regex level="fatal_oom" match="Can't calloc" source="both" />
    </stdio>
    <version_command><![CDATA[
    velocyto --version
    ]]></version_command>
    <command>
<![CDATA[
#import re

#if str($main.do) == "run10x":
  #if str($main.sample_definition.sample_definition_select) == "manual":
      #set sample = str($main.sample_definition.sample)
  #else:
      #set sample = re.sub('[^\w\-\s]', '_', str($main.BAM.element_identifier))
  #end if
  ## We need to reproduce cell ranger structure:
  mkdir -p '$sample/outs/filtered_gene_bc_matrices/whatever/' &&
  ln -s '${main.BAM}' '$sample/outs/possorted_genome_bam.bam' &&
  ln -s '${main.barcodes}' '$sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' &&
#else if str($main.do) in ['run', 'run-smartseq2']:
  #for $bam in $main.bamfiles:
    #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
    cp '$bam' '${input_name}.bam' &&
  #end for
#end if
velocyto

#if str($main.do) == "run":
run
  @LOOMOUT@
  #if str($main.b) != 'None':
    -b '$main.b'
  #end if
  #if str($main.m) != 'None':
    -m '$main.m' 
  #end if
  $main.c
  $main.U
  #if str($main.u):
    -u '$main.u'
  #end if
  $main.M
  -t '$main.t'
  @SAMTOOLS_OPTS@
  $verbosity
  *.bam
  '$main.gtffile'

#else if str($main.do) == "run10x":
run10x
  #if str($main.s) != 'None':
    -s '$main.s'
  #end if
  #if str($main.m) != 'None':
    -m '$main.m' 
  #end if
  $main.M
  -t '$main.t'
  @SAMTOOLS_OPTS@
  '$verbosity'
  '$sample'
  '$main.gtffile'
&& mv '$sample/velocyto/'*.loom 'output.loom'

#else if str($main.do) == "run-smartseq2":
run-smartseq2
   @LOOMOUT@
  #if str($main.m) != 'None':
    -m '$main.m' 
  #end if
  -t '$main.t'
  @SAMTOOLS_OPTS@
  '$verbosity'
  *.bam
  '$main.gtffile'

#else if str($main.do) == "run-dropest":
run-dropest
   @LOOMOUT@
  #if str($main.b) != 'None':
    -b '$main.b'
  #end if
  #if str($main.m) != 'None':
    -m '$main.m' 
  #end if
  -t '$main.t'
  @SAMTOOLS_OPTS@
  '$verbosity'
  '$main.bamfile'
  '$main.gtffile'

#else if str($main.do) == "dropest-bc-correct":
tools dropest-bc-correct
  -o '$barcodesout'
  '$main.bamfile'
  '$main.rfile'
#end if

]]>
    </command>
    <inputs>
        <conditional name="main"  >
            <param name="do" type="select" label="Pipeline"
                   help="" >
                <option value="run10x" selected="true">Analysis for a 10x Chromium Sample</option>
                <option value="run-smartseq2">Analysis on SmartSeq2 data (BAM file per cell)</option>
                <option value="run-dropest">Analysis on DropEst preprocessed data</option>
                <!-- the above are wrappers for the main "run" command -->
                <option value="run" >Analysis for other protocols</option>
                <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option>
            </param>
            <when value="run10x" >
                <conditional name="sample_definition">
                    <param name="sample_definition_select" type="select" label="How to set sample name" help="This name will appear as prefix of each cell barcode.">
                        <option value="manual">Manually</option>
                        <option value="identifier">Automatic (use identifier in history)</option>
                    </param>
                    <when value="manual">
                        <param name="sample" type="text" value="sample" label="sample name" help="">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits">
                                    <add value="_" />
                                </valid>
                            </sanitizer>
                            <validator type="regex">[0-9a-zA-Z_]+</validator>
                        </param>
                    </when>
                    <when value="identifier"/>
                </conditional>
                <param name="BAM" type="data" format="bam" label="BAM file including CB tag" help="Can be Cell ranger output or STAR solo output" />
                <param name="barcodes" type="data" format="tsv,tabular,txt" label="List of valid cell barcodes" help="Can be STAR solo barcodes output" />
                <param name="gtffile" type="data" format="gtf" label="GTF file" />
                <param argument="-s" type="data" format="csv" optional="true"
                       label="Metadata Table"
                       help="Table containing metadata of the various samples (csv formatted rows are samples and cols are entries)" />
                <expand macro="repmask" />
                <expand macro="notuniquemappings" />
                <expand macro="loomdtype" token_16_selected="true" token_32_selected="false" />
            </when>
            <when value="run-smartseq2" >
                <param name="bamfiles" type="data" format="bam" multiple="true"
                       label="BAM files" help="A BAM file for each cell. At least two required." />
                <param name="gtffile" type="data" format="gtf" label="GTF file" />
                <expand macro="repmask" />
                <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
            </when>
            <when value="run-dropest" >
                <param name="bamfile" type="data" format="bam" label="BAM file" help="BAM file" />
                <param name="gtffile" type="data" format="gtf" label="GTF file" />
                <expand macro="bcffile" />
                <expand macro="repmask" />
                <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
            </when>
            <when value="run" >
                <param name="bamfiles" type="data" format="bam" label="BAM file" help="BAM file" multiple="true"/>
                <param name="gtffile" type="data" format="gtf" label="GTF file" />
                <expand macro="bcffile" />
                <expand macro="repmask" />
                <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
                       label="One file per cell?"
                       help="If this flag is used every bamfile passed is interpreted as an independent cell, otherwise multiple files are interpreted as batch of different cells to be analyzed together. Important: cells reads should not be distributed over multiple bamfiles is not supported!! (default: off)" />
                <param argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false"
                       label="Without UMI?"
                       help="If this flag is used the data is assumed UMI-less and reads are counted instead of molecules (default: off)" />
                <param argument="-u" type="text" value="" optional="true"
                       label="UMI extension"
                       help="In case UMI is too short to guarantee uniqueness (without information from the ampping) set this parameter to chr, Gene ro [N]bp If set to chr the mapping position (binned to 10Gb intervals) will be appended to UB (ideal for InDrops+dropEst). If set to Gene then the GX tag will be appended to the UB tag. If set to [N]bp the first N bases of the sequence will be used to extend UB (ideal for STRT). (Default: no)" />
                <expand macro="notuniquemappings" />
                <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
            </when>
            <when value="dropest-bc-correct" >
                <param name="bamfile" type="data" format="BAM"
                       label="Bam file with sorted reads obtained from DropEst" />
                <param name="rfile" type="data" format="rds"
                       label="R dump RDS file generated from DropEst" />
            </when>
        </conditional>
        <param name="verbosity" type="select" label="verbosity level">
            <option value="-v">show only warning</option>
            <option value="-vv" selected="true">show warning and info</option>
            <option value="-vvv">show warning, info and debug</option>
        </param>
    </inputs>
    <outputs>
        <data format="loom" name="samples" from_work_dir="output.loom"/>
        <data name="barcodesout" format="txt" label="${tool.name} on ${on_string}: Barcodes file" >
            <filter>main['do']=='dropest-bc-correct'</filter>
        </data>
    </outputs>
    <tests>
      <!-- Test 1 10x -->
      <test expect_num_outputs="1">
          <conditional name="main">
              <param name="do" value="run10x"/>
              <conditional name="sample_definition">
                  <param name="sample_definition_select" value="manual"/>
                  <param name="sample" value="sample"/>
              </conditional>
              <param name="BAM" value="STARsolo_allSAMat.bam"/>
              <param name="barcodes" value="barcodes.tsv"/>
              <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
              <param name="M" value="false"/>
              <param name="t" value="uint16"/>
          </conditional>
          <output name="samples">
              <assert_contents>
                  <has_size value="25996" delta="3000"/>
              </assert_contents>
              <metadata name="row_attrs_count" value="6" />
              <metadata name="layers_count" value="3" />
              <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
              <metadata name="col_attrs_count" value="1" />
              <metadata name="col_attrs_names" value="CellID" />
          </output>
          <assert_command>
              <has_text text="sample"/>
          </assert_command>
          <assert_stdout>
              <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
          </assert_stdout>
      </test>
      <!-- Test 2 run single bam as single cell -->
      <test expect_num_outputs="1">
          <conditional name="main">
              <param name="do" value="run"/>
              <param name="bamfiles" value="STARsolo_allSAMat.bam"/>
              <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
              <param name="c" value="true"/>
              <param name="U" value="true"/>
              <param name="M" value="false"/>
              <param name="t" value="uint16"/>
          </conditional>
          <output name="samples">
              <assert_contents>
                  <has_size value="25927" delta="3000"/>
              </assert_contents>
              <metadata name="row_attrs_count" value="6" />
              <metadata name="layers_count" value="3" />
              <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
              <metadata name="col_attrs_count" value="1" />
              <metadata name="col_attrs_names" value="CellID" />
          </output>
          <assert_stdout>
            <has_text text="Counting for batch 1, containing 1 cells and 716 reads"/>
          </assert_stdout>
      </test>
      <!-- Test 3 run single bam as single cell with 2 bam -->
      <test expect_num_outputs="1">
          <conditional name="main">
              <param name="do" value="run"/>
              <param name="bamfiles" value="STARsolo_allSAMat.bam,STARsolo_allSAMat_copy.bam"/>
              <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
              <param name="c" value="true"/>
              <param name="U" value="true"/>
              <param name="M" value="false"/>
              <param name="t" value="uint16"/>
          </conditional>
          <output name="samples">
              <assert_contents>
                  <has_size value="26384" delta="3000"/>
              </assert_contents>
              <metadata name="row_attrs_count" value="6" />
              <metadata name="layers_count" value="3" />
              <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
              <metadata name="col_attrs_count" value="1" />
              <metadata name="col_attrs_names" value="CellID" />
          </output>
          <assert_stdout>
            <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/>
          </assert_stdout>
      </test>
      <!-- Test 4 10x indentifyer -->
      <test expect_num_outputs="1">
          <conditional name="main">
              <param name="do" value="run10x"/>
              <conditional name="sample_definition">
                  <param name="sample_definition_select" value="identifier"/>
              </conditional>
              <param name="BAM" value="STARsolo_allSAMat.bam"/>
              <param name="barcodes" value="barcodes.tsv"/>
              <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
              <param name="M" value="false"/>
              <param name="t" value="uint16"/>
          </conditional>
          <output name="samples">
              <assert_contents>
                  <has_size value="25996" delta="3000"/>
              </assert_contents>
              <metadata name="row_attrs_count" value="6" />
              <metadata name="layers_count" value="3" />
              <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
              <metadata name="col_attrs_count" value="1" />
              <metadata name="col_attrs_names" value="CellID" />
          </output>
          <assert_command>
              <has_text text="STARsolo_allSAMat"/>
              <not_has_text text="sample"/>
          </assert_command>
          <assert_stdout>
              <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
          </assert_stdout>
      </test>
    </tests>
    <help><![CDATA[
Requirements on the input files

velocyto assumes that the bam file that is passed to the CLI contains a set of information and that some upstream analysis was performed on them already. In particular the bam file will have to:

    Be sorted by mapping position.
    Represents either a single sample (multiple cells prepared using a certain barcode set in a single experiment) or single cell.
    Contain an error corrected cell barcodes as a TAG named CB or XC.
    Contain an error corrected molecular barcodes as a TAG named UB or XM.

Note

For SmartSeq2 bam files (3) and (4) are not required because it consists of one bam file per cell and no umi are present.

velocyto assumes that the gtf file follows the GENCODE gtf format description. However some mandatory field are relaxed to extend compatibility to a wider set of gtf files. In particular the gtf file will have to:

    Contain the 3rd column entry feature-type. Note that only the exon entry of the gtf file marked as exon in this column will be considered and therefore the requirements below only apply to the ``exon`` labeled lines.
    Contain, in the 9th column, the key-value pair transcript_id, containing an unique identified for the transcript model.
    Contain, in the 9th column, the key-value pair transcript_name (Optional, if not present it will be set to the value of transcript_id)
    Contain, in the 9th column, the key-value pair gene_id, containing an unique identified for the gene.
    Contain, in the 9th column, the key-value pair gene_name (Optional, if not present it will be set to the value of gene_id)
    Contain, in the 9th column, the key-value pair exon_number (Recommended but optional, if not provided velocyto will sort exons in memory and number them)

    ]]>
    </help>
    <expand macro="citations"/>
</tool>