diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 64693929..69d9aeda 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -4,3 +4,4 @@ FOR CONTRIBUTOR: * [ ] - This PR adds a new tool or tool collection * [ ] - This PR updates an existing tool or tool collection * [ ] - This PR does something else (explain below) +* [ ] - Tools added/updated by this PR (if any) comply with the [Naming and Annotation Conventions for Tools in the Image Community in Galaxy](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md) (or please explain why they do not) diff --git a/README.md b/README.md index 8a9a6332..433cc311 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ -[![Build Status](https://travis-ci.org/BMCV/galaxy-image-analysis.svg?branch=master)](https://travis-ci.org/BMCV/galaxy-image-analysis) +[![Galaxy Tool Linting and Tests for push and PR](https://github.com/BMCV/galaxy-image-analysis/actions/workflows/pr.yaml/badge.svg?branch=master)](https://github.com/BMCV/galaxy-image-analysis/actions/workflows/pr.yaml?query=branch:master) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.jbiotec.2017.07.019-blue)](https://doi.org/10.1016/j.jbiotec.2017.07.019) [![Chat on matrix](https://img.shields.io/badge/chat_on-matrix-green)](https://matrix.to/#/#galaxyproject_imaging:matrix.org) +[![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAASCAYAAABB7B6eAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAACXBIWXMAAAsTAAALEwEAmpwYAAACC2lUWHRYTUw6Y29tLmFkb2JlLnhtcAAAAAAAPHg6eG1wbWV0YSB4bWxuczp4PSJhZG9iZTpuczptZXRhLyIgeDp4bXB0az0iWE1QIENvcmUgNS40LjAiPgogICA8cmRmOlJERiB4bWxuczpyZGY9Imh0dHA6Ly93d3cudzMub3JnLzE5OTkvMDIvMjItcmRmLXN5bnRheC1ucyMiPgogICAgICA8cmRmOkRlc2NyaXB0aW9uIHJkZjphYm91dD0iIgogICAgICAgICAgICB4bWxuczp0aWZmPSJodHRwOi8vbnMuYWRvYmUuY29tL3RpZmYvMS4wLyI+CiAgICAgICAgIDx0aWZmOlJlc29sdXRpb25Vbml0PjI8L3RpZmY6UmVzb2x1dGlvblVuaXQ+CiAgICAgICAgIDx0aWZmOkNvbXByZXNzaW9uPjE8L3RpZmY6Q29tcHJlc3Npb24+CiAgICAgICAgIDx0aWZmOk9yaWVudGF0aW9uPjE8L3RpZmY6T3JpZW50YXRpb24+CiAgICAgICAgIDx0aWZmOlBob3RvbWV0cmljSW50ZXJwcmV0YXRpb24+MjwvdGlmZjpQaG90b21ldHJpY0ludGVycHJldGF0aW9uPgogICAgICA8L3JkZjpEZXNjcmlwdGlvbj4KICAgPC9yZGY6UkRGPgo8L3g6eG1wbWV0YT4KD0UqkwAAAn9JREFUOBGlVEuLE0EQruqZiftwDz4QYT1IYM8eFkHFw/4HYX+GB3/B4l/YP+CP8OBNTwpCwFMQXAQPKtnsg5nJZpKdni6/6kzHvAYDFtRUT71f3UwAEbkLch9ogQxcBwRKMfAnM1/CBwgrbxkgPAYqlBOy1jfovlaPsEiWPROZmqmZKKzOYCJb/AbdYLso9/9B6GppBRqCrjSYYaquZq20EUKAzVpjo1FzWRDVrNay6C/HDxT92wXrAVCH3ASqq5VqEtv1WZ13Mdwf8LFyyKECNbgHHAObWhScf4Wnj9CbQpPzWYU3UFoX3qkhlG8AY2BTQt5/EA7qaEPQsgGLWied0A8VKrHAsCC1eJ6EFoUd1v6GoPOaRAtDPViUr/wPzkIFV9AaAZGtYB568VyJfijV+ZBzlVZJ3W7XHB2RESGe4opXIGzRTdjcAupOK09RA6kzr1NTrTj7V1ugM4VgPGWEw+e39CxO6JUw5XhhKihmaDacU2GiR0Ohcc4cZ+Kq3AjlEnEeRSazLs6/9b/kh4eTC+hngE3QQD7Yyclxsrf3cpxsPXn+cFdenF9aqlBXMXaDiEyfyfawBz2RqC/O9WF1ysacOpytlUSoqNrtfbS642+4D4CS9V3xb4u8P/ACI4O810efRu6KsC0QnjHJGaq4IOGUjWTo/YDZDB3xSIxcGyNlWcTucb4T3in/3IaueNrZyX0lGOrWndstOr+w21UlVFokILjJLFhPukbVY8OmwNQ3nZgNJNmKDccusSb4UIe+gtkI+9/bSLJDjqn763f5CQ5TLApmICkqwR0QnUPKZFIUnoozWcQuRbC0Km02knj0tPYx63furGs3x/iPnz83zJDVNtdP3QAAAABJRU5ErkJggg==)](https://imaging.usegalaxy.eu) # Galaxy Image Analysis diff --git a/tools/overlay_images/overlay_images.xml b/tools/overlay_images/overlay_images.xml index d58bdb6f..053d1b13 100644 --- a/tools/overlay_images/overlay_images.xml +++ b/tools/overlay_images/overlay_images.xml @@ -1,4 +1,4 @@ - + operation_3443 @@ -15,7 +15,12 @@ - + + method_option['method'] != 'seg_contour' + + + method_option['method'] == 'seg_contour' + - + - + - + - + - + - + - + - + diff --git a/tools/overlay_images/test-data/test3.tif b/tools/overlay_images/test-data/test3.png similarity index 100% rename from tools/overlay_images/test-data/test3.tif rename to tools/overlay_images/test-data/test3.png diff --git a/tools/overlay_images/test-data/test4.png b/tools/overlay_images/test-data/test4.png new file mode 100644 index 00000000..983170d1 Binary files /dev/null and b/tools/overlay_images/test-data/test4.png differ diff --git a/tools/overlay_images/test-data/test4.tif b/tools/overlay_images/test-data/test4.tif deleted file mode 100644 index 43254e38..00000000 Binary files a/tools/overlay_images/test-data/test4.tif and /dev/null differ