initialise open version of crconverter script

#!/bin/bash

######convert version#####

crconverterversion="3.1.1.90001"

##########

#####cellranger version#####

cellrangerpath=`which cellranger` #location of cellranger

if [[ -z $cellrangerpath ]]; then

    echo "cellranger command is not found."

    exit 1

fi

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

##########

#####declare variables#####

SOURCE="${BASH_SOURCE[0]}"

##########

#####usage statement#####

statement='

crconverter

 Usage:

        crconverter <name> <type> [options]

    crconverter -h | --help | --version

'

options='

Options:

        --inpath=PATH          Path to a completed pipestance. crconvert will attempt find inputs automatically by filename

                               Explicit setting of input using other flags will override inputs found with --inpath

    --output=PATH      

    --pipestance=PATH 

    --metrics=PATH     

    --analysis=PATH    

    --matrix=PATH      

    --aggregation=PATH 

        --gemgroups=PATH   

        --contiginfo=PATH

        --peaks=PATH

        --fragmentsindex=PATH

        --geneannotations=PATH

        --geneannotationtypes=TYPES

    --description=DESC 

    -h --help          

    --version          

This is an open-source implementation of crconverter.

This is only intended for testing open-source implementations

of cellranger and may not produce the same results as

software produced by 10x Genomics. We recommend the

supported software be used for other purposes.

The code in this repository is licensed under the MIT License.

'

##########

#variable optionsname=false

name=$1

type=$2

read1=()

read2=()

SAMPLE=""

LANE=()

id=""

description=""

reference=""

ncells=""

chemistry="SC3Pv2"

jobmode="local"

ncores=""

mem=""

percelldata=false

next=false

end=false

# crconverter tiny SC_RNA_COUNTER_CS --matrix /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u00fa679091/files/filtered_matrices_h5.h5 \

# --analysis /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u00fa67911f/files/analysis/analysis.h5 \ 

# --output /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/output_for_cloupe.cloupe \ 

# --description CellRangerTest \ 

# --metrics /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/join-u00fa679151/files/metrics_summary_json.json \

# --gemgroups /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/gem_group_index_json.json

for op in "${@:3}"; do

    if $next; then

        next=false;

        continue;

    fi

    case "$op" in

          --inpath)

            shift

            if [[ "$1" != "" ]]; then

                inpath="${1/%\//}"

                next=true

                shift

            else

                echo "Explicit setting of input using other flags will override inputs found with --inpath"

            fi

            ;;

           --description)

            shift

            if [[ "$1" != "" ]]; then

                description="${1/%\//}"

                next=true

                shift

            else

                echo "Error: value missing for --description"

                exit 1

            fi

            ;;

        -v|--version)

            end=true

            version=true

            echo "$crconverterversion"

            exit 0

            ;;

        -h|--help)

            end=true

            usage=true

            help=true

            echo "$statement"

            echo "$options"

            exit 0

            ;;

       --verbose)

            echo "debugging mode activated"

            verbose=true

            next=false

            shift

            ;;

        -*)

            echo "$statement"

            exit 1

            ;;

    esac

done

##########

if [[ -z $1 ]]; then

    echo "$statement"

    exit 1

fi

if [[ -z $version ]]; then

    echo "$crconverterversion"

    exit 0

fi

##########

echo "Cloupe File not generated"

exit 0

#Wrote .cloupe file to /home/tom/datasets/20190717_Plant_Protoplast_fiveprime_HiSeq/test_AtRTD2_P09_PE/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u4b566787c3/files/output_for_cloupe.cloupe

# crconverter tiny SC_RNA_COUNTER_CS --matrix /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u00fa679091/files/filtered_matrices_h5.h5 \

# --analysis /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u00fa67911f/files/analysis/analysis.h5 \ 

# --output /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/output_for_cloupe.cloupe \ 

# --description CellRangerTest \ 

# --metrics /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/join-u00fa679151/files/metrics_summary_json.json \

# --gemgroups /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/gem_group_index_json.json