From b5716a576805fc125d25f41d8074a5d4ab59ed45 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 7 Oct 2023 23:38:57 +0200 Subject: [PATCH] chore: consistently add xml to all relevant md codefences --- submit/analyses/bionano-maps.md | 18 ++++++++-------- submit/analyses/pacbio-methylation.md | 18 ++++++++-------- submit/analyses/read-alignments.md | 16 +++++++------- submit/analyses/sequence-annotation.md | 16 +++++++------- submit/general-guide/programmatic.md | 30 +++++++++++++------------- submit/general-guide/webin-cli.md | 2 +- update/metadata/programmatic-read.md | 12 +++++------ update/metadata/programmatic-sample.md | 2 +- update/metadata/programmatic-study.md | 2 +- 9 files changed, 58 insertions(+), 58 deletions(-) diff --git a/submit/analyses/bionano-maps.md b/submit/analyses/bionano-maps.md index 38ed96f1..8dc115a1 100644 --- a/submit/analyses/bionano-maps.md +++ b/submit/analyses/bionano-maps.md @@ -59,13 +59,13 @@ Optical maps must be associated with a study and a sample. An analysis points to the study it is part of using the `` element. This can be done either by using an accession: -``` +```xml ``` or a name within the submitter's account: -``` +```xml ``` @@ -100,7 +100,7 @@ This submits the data files into the archive. For example: -``` +```xml @@ -110,14 +110,14 @@ For example: If the files are uploaded to the root directory then simply enter the file name in the Analysis XML when referring to it: -``` +```xml ``` If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name with the name of the subdirectory: -``` +```xml ``` @@ -136,7 +136,7 @@ For full details of the BioNano data files please refer to [Bionano Solve](https All other metadata used to describe the analysis can be provided using `ANALYSIS_ATTRIBUTE` elements in the XML: -``` +```xml library preparation date 2010-08 @@ -148,7 +148,7 @@ the XML: Once you have created your analysis XML, you need an accompanying submission XML in a separate file to tell ENA what actions you would like to take for your submission. -``` +```xml @@ -181,7 +181,7 @@ Please provide your Webin submission account credentials using the `username` an After running the command above a receipt XML is returned. It will look like the one below: -``` +```xml @@ -215,7 +215,7 @@ contain the accession numbers of the objects that you have submitted. Note the message in the receipt: -``` +```xml This submission is a TEST submission and will be discarded within 24 hours ``` diff --git a/submit/analyses/pacbio-methylation.md b/submit/analyses/pacbio-methylation.md index 03909722..1992f8cc 100644 --- a/submit/analyses/pacbio-methylation.md +++ b/submit/analyses/pacbio-methylation.md @@ -64,13 +64,13 @@ Analysis type `` is use for submitting PacBio methylation d An analysis points to the study it is part of using the `` element. This can be done either by using an accession: -``` +```xml ``` or a name within the submitter's account: -``` +```xml ``` @@ -105,7 +105,7 @@ This submits the data files into the archive. For example: -``` +```xml @@ -119,14 +119,14 @@ For example: If the files are uploaded to the root directory then simply enter the file name in the Analysis XML when referring to it: -``` +```xml ``` If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name with the name of the subdirectory: -``` +```xml ``` @@ -140,7 +140,7 @@ and how to generate them, please refer to All other metadata used to describe the analysis can be provided using `ANALYSIS_ATTRIBUTE` elements in the XML: -``` +```xml library preparation date 2010-08 @@ -152,7 +152,7 @@ the XML: Once you have created your analysis XML, you need an accompanying submission XML in a separate file to tell ENA what actions you would like to take for your submission. -``` +```xml @@ -185,7 +185,7 @@ Please provide your Webin submission account credentials using the `username` an After running the command above a receipt XML is returned. It will look like the one below: -``` +```xml @@ -219,7 +219,7 @@ contain the accession numbers of the objects that you have submitted. Note the message in the receipt: -``` +```xml This submission is a TEST submission and will be discarded within 24 hours ``` diff --git a/submit/analyses/read-alignments.md b/submit/analyses/read-alignments.md index c9541700..79925229 100644 --- a/submit/analyses/read-alignments.md +++ b/submit/analyses/read-alignments.md @@ -102,13 +102,13 @@ one or more samples. An analysis points to the study it is part of using the `` element. This can be done either by using an accession: -``` +```xml ``` or a name within the submitter's account: -``` +```xml ``` @@ -143,7 +143,7 @@ This submits the data files into the archive. For example: -``` +```xml @@ -153,14 +153,14 @@ For example: If the files are uploaded to the root directory then simply enter the file name in the Analysis XML when referring to it: -``` +```xml ``` If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name with the name of the subdirectory: -``` +```xml ``` @@ -181,7 +181,7 @@ the XML: Once you have created your analysis XML, you need an accompanying submission XML in a separate file to tell ENA what actions you would like to take for your submission. -``` +```xml @@ -214,7 +214,7 @@ Please provide your Webin submission account credentials using the `username` an After running the command above a receipt XML is returned. It will look like the one below: -``` +```xml @@ -248,7 +248,7 @@ contain the accession numbers of the objects that you have submitted. Note the message in the receipt: -``` +```xml This submission is a TEST submission and will be discarded within 24 hours ``` diff --git a/submit/analyses/sequence-annotation.md b/submit/analyses/sequence-annotation.md index b1af8db7..8c7f3aa2 100644 --- a/submit/analyses/sequence-annotation.md +++ b/submit/analyses/sequence-annotation.md @@ -58,13 +58,13 @@ Sequence annotation analyses must be associated with a study and at most one sam An analysis points to the study it is part of using the `` element. This can be done either by using an accession: -``` +```xml ``` or a name within the submitter's account: -``` +```xml ``` @@ -99,7 +99,7 @@ This submits the data files into the archive. For example: -``` +```xml @@ -109,14 +109,14 @@ For example: If the files are uploaded to the root directory then simply enter the file name in the Analysis XML when referring to it: -``` +```xml ``` If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name with the name of the subdirectory: -``` +```xml ``` @@ -137,7 +137,7 @@ the XML: Once you have created your analysis XML, you need an accompanying submission XML in a separate file to tell ENA what actions you would like to take for your submission. -``` +```xml @@ -170,7 +170,7 @@ Please provide your Webin submission account credentials using the `username` an After running the command above a receipt XML is returned. It will look like the one below: -``` +```xml @@ -204,7 +204,7 @@ contain the accession numbers of the objects that you have submitted. Note the message in the receipt: -``` +```xml This submission is a TEST submission and will be discarded within 24 hours ``` diff --git a/submit/general-guide/programmatic.md b/submit/general-guide/programmatic.md index 59218f66..bd266aa2 100644 --- a/submit/general-guide/programmatic.md +++ b/submit/general-guide/programmatic.md @@ -115,7 +115,7 @@ The most commonly used submission actions are listed below. The `ADD` action is used when submitting new objects. A corresponding submission XML will look like: -``` +```xml @@ -134,7 +134,7 @@ they refer to are made public. A release date can be provided for studies by using the `HOLD` action together with the `ADD` action: -``` +```xml @@ -157,7 +157,7 @@ time. A study can be made immediately public by using `RELEASE` action with the study accession number: -``` +```xml @@ -171,7 +171,7 @@ A study can be made immediately public by using `RELEASE` action with the study You can update the release date of a study, project or sample by using the `HOLD` action with a new release date.: -``` +```xml @@ -191,7 +191,7 @@ The new release date must be not more than two years in the future. IF `RELEASE` action is provided without a target attribute then all submitted studies, projects and samples will become immediately public. -``` +```xml @@ -208,7 +208,7 @@ Run, experiment and analysis objects will become public as long as the studies o The `MODIFY` action is used when updating existing objects. A corresponding submission XML will look like: -``` +```xml @@ -229,7 +229,7 @@ in the initial submission. Below is an extract of an study XML which contains an accession number: -``` +```xml ... @@ -237,7 +237,7 @@ Below is an extract of an study XML which contains an accession number: Below is an extract of an study XML which contains an alias: -``` +```xml ... @@ -248,7 +248,7 @@ Below is an extract of an study XML which contains an alias: The `VALIDATE` action is used when validating a submission without actually creating or updating any objects. It can be used together with the `ADD` action (default): -``` +```xml @@ -263,7 +263,7 @@ updating any objects. It can be used together with the `ADD` action (default): Or with the `MODIFY` action: -``` +```xml @@ -288,7 +288,7 @@ that the `CANCEL` action will be propagated from studies to all associated exper Below is an example of a submission XML used to cancel objects: -``` +```xml @@ -305,8 +305,8 @@ that contains all the issued accession numbers. This is expecially useful in cas submission request times out before it has as completed. The submission process will continue neverthless and the issued accession numbers can be later requested using the `RECEIPT` action. -``` -SUBMISSION_SET> +```xml + @@ -364,7 +364,7 @@ publication. An example of a successful run submission: -``` +```xml @@ -378,7 +378,7 @@ within the `RUN` block. If the submission was not successful the Receipt XML will contain the error messages within the `MESSAGES` block: -``` +```xml ... diff --git a/submit/general-guide/webin-cli.md b/submit/general-guide/webin-cli.md index 6fb8b362..2846d02c 100644 --- a/submit/general-guide/webin-cli.md +++ b/submit/general-guide/webin-cli.md @@ -197,7 +197,7 @@ The manifest file has two columns separated by a colon: For example, the following manifest file represents a multi-fastq submission for single-cell data: -``` +```json { "study": "TODO", "sample": "TODO", diff --git a/update/metadata/programmatic-read.md b/update/metadata/programmatic-read.md index da0231fb..295f9d18 100644 --- a/update/metadata/programmatic-read.md +++ b/update/metadata/programmatic-read.md @@ -3,7 +3,7 @@ The main difference between programmatically creating new experiment and runs and updating existing ones is that the `MODIFY` action should be used instead of the `ADD` action: -``` +```xml @@ -28,7 +28,7 @@ Typical reasons for updating experiment XMLs include: - Change the library descriptor: -``` +```xml RNA-Seq @@ -43,19 +43,19 @@ Typical reasons for updating experiment XMLs include: - Move the experiment to a different study by changing the `STUDY_REF`: -``` +```xml ``` - Associate the experiment with a different sample by changing the `SAMPLE_DESCRIPTOR`: -``` +```xml ``` - Include more information in experiment attributes: -``` +```xml library preparation date 2010-08 @@ -65,7 +65,7 @@ Typical reasons for updating experiment XMLs include: ## Reasons for Updating Run XML Most common reason for updating run XMLs is to change the file checksum: -``` +```xml ``` diff --git a/update/metadata/programmatic-sample.md b/update/metadata/programmatic-sample.md index b64f3740..f6a2ef48 100644 --- a/update/metadata/programmatic-sample.md +++ b/update/metadata/programmatic-sample.md @@ -3,7 +3,7 @@ The main difference between programmatically creating new samples and updating existing ones is that the `MODIFY` action should be used instead of the `ADD` action: -``` +```xml diff --git a/update/metadata/programmatic-study.md b/update/metadata/programmatic-study.md index 57677a37..8f998816 100644 --- a/update/metadata/programmatic-study.md +++ b/update/metadata/programmatic-study.md @@ -3,7 +3,7 @@ The main difference between programmatically creating new studies and updating existing ones is that the `MODIFY` action should be used instead of the `ADD` action: -``` +```xml