changeset 17:52a13f003b2d draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit b5d08d89e75e2dbfa03f74e45aa6baa465582eee

--- a/run_segalign_diagonal_partition	Tue Jul 30 17:19:56 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit
-set -o nounset
-set -o pipefail
-
-##
-## parse arguments
-##
-
-SEGALIGN_ARGS=()
-
-MAX_SEGMENT_SIZE=""
-OUTPUT_FILENAME=""
-LASTZ_COMMAND_FILE="lastz_commands.txt"
-HELP=0
-
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        --help)
-            HELP=1
-            shift
-            ;;
-        --max_segments)
-            MAX_SEGMENT_SIZE="$2"
-            shift 2
-            ;;
-        --output)
-            OUTPUT_FILENAME=$(readlink -f "$2")
-            shift 2
-            ;;
-        --tool_directory)
-            TOOL_DIRECTORY="$2"
-            shift 2
-            ;;
-        *)
-            SEGALIGN_ARGS+=("$1")
-            shift
-    esac
-done
-
-set -- "${SEGALIGN_ARGS[@]}"
-
-##
-## check arguments
-##
-
-if [[ $# == 0 || "$HELP" == "1" ]]; then
-    segalign --help
-    exit 0
-fi
-
-if [[ $# -lt 2 ]]; then
-    echo "run_segalign_diagonal_partition: missing target and query sequences" 1>&2
-    exit 1
-fi
-
-ref_path=$(readlink -f "$1")
-test -e "$ref_path" || {
-    echo "run_segalign_diagonal_partition: target file \"$ref_path\" does not exist" 1>&2
-    exit 1
-}
-query_path=$(readlink -f "$2")
-test -e "$query_path" || {
-    echo "run_segalign_diagonal_partition: query file \"$query_path\" does not exist" 1>&2
-    exit 1
-}
-shift 2
-
-DATA_FOLDER="data"
-mkdir -p "$DATA_FOLDER" || {
-    echo "run_segalign_diagonal_partition: cannont create data directory \"$DATA_FOLDER\"" 1>&2
-    exit 1
-}
-
-cd $DATA_FOLDER/..
-echo ""
-echo "Converting fasta files to 2bit format" 1>&2
-
-##
-## convert target and query to 2bit
-##
-faToTwoBit <(gzip -cdfq "$ref_path") "$DATA_FOLDER/ref.2bit" || {
-    echo "run_segalign_diagonal_partition: cannot convert \"$ref_path\" to 2bit" 1>&2
-    exit 1
-}
-faToTwoBit <(gzip -cdfq "$query_path") "$DATA_FOLDER/query.2bit" || {
-    echo "run_segalign_diagonal_partition: cannont convert \"$ref_path\" to 2bit" 1>&2
-    exit 1
-}
-
-
-
-time {
-    while IFS= read -r line; do
-        python "$TOOL_DIRECTORY/diagonal_partition.py" $MAX_SEGMENT_SIZE $line >> $LASTZ_COMMAND_FILE || {
-            echo "run_segalign_diagonal_partition: failed: diagonal_partition.py $MAX_SEGMENT_SIZE $line" 1>&2
-            exit 1
-        }
-        # segalign sort writes out the partitioned segment files to the working
-        # directory and prints the modified lastz commands.
-    done < <(stdbuf -oL segalign $ref_path $query_path "${DATA_FOLDER}/" "$@" ) # segalign begins running in this line, 
-} 1>&2 # and every newline written to stdout, get assigned to $line which
-       # gets sent to diagonal_partition for diagonal partitioning
-
-exit 0
-