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feat: consistently add xml to all relevant md codefences for syntax highlighting #163

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18 changes: 9 additions & 9 deletions submit/analyses/bionano-maps.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 `<STUDY_REF>` element.
This can be done either by using an accession:

```
```xml
<STUDY_REF accession="ERP123456"/>
```

or a name within the submitter's account:

```
```xml
<STUDY_REF refname="mantis_religiosa"/>
```

Expand Down Expand Up @@ -100,7 +100,7 @@ This submits the data files into the archive.

For example:

```
```xml
<FILES>
<FILE filename="Euclidium_syriacum.Run-01.bnx.gz" filetype="BioNano_native"
checksum_method="MD5" checksum="ff9dd3a61d88092cb74ff8227ed725aa"/>
Expand All @@ -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
<FILE filename="a.bnx" ... />
```

If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name
with the name of the subdirectory:

```
```xml
<FILE filename="mantis_religiosa/a.bnx" ... />
```

Expand All @@ -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
<ANALYSIS_ATTRIBUTE>
<TAG>library preparation date</TAG>
<VALUE>2010-08</VALUE>
Expand All @@ -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
<SUBMISSION>
<ACTIONS>
<ACTION>
Expand Down Expand Up @@ -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
<?xml version="1.0" encoding="UTF-8"?>
<RECEIPT receiptDate="2017-08-11T15:07:36.746+01:00" submissionFile="sub.xml" success="true">
<ANALYSIS accession="ERZ0151578" alias="08-1736" status="PRIVATE"/>
Expand Down Expand Up @@ -215,7 +215,7 @@ contain the accession numbers of the objects that you have submitted.

Note the message in the receipt:

```
```xml
<INFO>This submission is a TEST submission and will be discarded within 24 hours</INFO>
```

Expand Down
18 changes: 9 additions & 9 deletions submit/analyses/pacbio-methylation.md
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Original file line number Diff line number Diff line change
Expand Up @@ -64,13 +64,13 @@ Analysis type `<SEQUENCE_ANNOTATION>` is use for submitting PacBio methylation d
An analysis points to the study it is part of using the `<STUDY_REF>` element.
This can be done either by using an accession:

```
```xml
<STUDY_REF accession="ERP123456"/>
```

or a name within the submitter's account:

```
```xml
<STUDY_REF refname="mantis_religiosa"/>
```

Expand Down Expand Up @@ -105,7 +105,7 @@ This submits the data files into the archive.

For example:

```
```xml
<FILES>
<FILE filename="data-motifs.gff.gz" filetype="gff" checksum_method="MD5"
checksum="7fd0cf4f550fd836758bfc242894a8fe"/>
Expand All @@ -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
<FILE filename="a.gff.gz"" ... />
```

If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name
with the name of the subdirectory:

```
```xml
<FILE filename="mantis_religiosa/a.gff.gz"" ... />
```

Expand All @@ -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
<ANALYSIS_ATTRIBUTE>
<TAG>library preparation date</TAG>
<VALUE>2010-08</VALUE>
Expand All @@ -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
<SUBMISSION>
<ACTIONS>
<ACTION>
Expand Down Expand Up @@ -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
<?xml version="1.0" encoding="UTF-8"?>
<RECEIPT receiptDate="2017-08-11T15:07:36.746+01:00" submissionFile="sub.xml" success="true">
<ANALYSIS accession="ERZ0151578" alias="08-1736" status="PRIVATE"/>
Expand Down Expand Up @@ -219,7 +219,7 @@ contain the accession numbers of the objects that you have submitted.

Note the message in the receipt:

```
```xml
<INFO>This submission is a TEST submission and will be discarded within 24 hours</INFO>
```

Expand Down
16 changes: 8 additions & 8 deletions submit/analyses/read-alignments.md
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,13 +102,13 @@ one or more samples.
An analysis points to the study it is part of using the `<STUDY_REF>` element.
This can be done either by using an accession:

```
```xml
<STUDY_REF accession="ERP123456"/>
```

or a name within the submitter's account:

```
```xml
<STUDY_REF refname="mantis_religiosa"/>
```

Expand Down Expand Up @@ -143,7 +143,7 @@ This submits the data files into the archive.

For example:

```
```xml
<FILES>
<FILE checksum="bafe0ed9be5c0f8515cdc4ac514d24af" checksum_method="MD5"
filename="AD0370_C.bam" filetype="bam"/>
Expand All @@ -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
<FILE filename="a.bam" ... />
```

If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name
with the name of the subdirectory:

```
```xml
<FILE filename="mantis_religiosa/a.bam" ... />
```

Expand All @@ -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
<SUBMISSION>
<ACTIONS>
<ACTION>
Expand Down Expand Up @@ -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
<?xml version="1.0" encoding="UTF-8"?>
<RECEIPT receiptDate="2017-08-11T15:07:36.746+01:00" submissionFile="sub.xml" success="true">
<ANALYSIS accession="ERZ0151578" alias="08-1736" status="PRIVATE"/>
Expand Down Expand Up @@ -248,7 +248,7 @@ contain the accession numbers of the objects that you have submitted.

Note the message in the receipt:

```
```xml
<INFO>This submission is a TEST submission and will be discarded within 24 hours</INFO>
```

Expand Down
16 changes: 8 additions & 8 deletions submit/analyses/sequence-annotation.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 `<STUDY_REF>` element.
This can be done either by using an accession:

```
```xml
<STUDY_REF accession="ERP123456"/>
```

or a name within the submitter's account:

```
```xml
<STUDY_REF refname="mantis_religiosa"/>
```

Expand Down Expand Up @@ -99,7 +99,7 @@ This submits the data files into the archive.

For example:

```
```xml
<FILES>
<FILE filename="STR_for_YF03059_20151228.tab.gz" filetype="tab" checksum_method="MD5"
checksum="9f2976d079c10b111669b32590d1eb3e"/>
Expand All @@ -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
<FILE filename="a.tab.gz"" ... />
```

If the files are uploaded into a subdirectory (e.g. `mantis_religiosa`) then prefix the file name
with the name of the subdirectory:

```
```xml
<FILE filename="mantis_religiosa/a.tab.gz"" ... />
```

Expand All @@ -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
<SUBMISSION>
<ACTIONS>
<ACTION>
Expand Down Expand Up @@ -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
<?xml version="1.0" encoding="UTF-8"?>
<RECEIPT receiptDate="2017-08-11T15:07:36.746+01:00" submissionFile="sub.xml" success="true">
<ANALYSIS accession="ERZ0151578" alias="08-1736" status="PRIVATE"/>
Expand Down Expand Up @@ -204,7 +204,7 @@ contain the accession numbers of the objects that you have submitted.

Note the message in the receipt:

```
```xml
<INFO>This submission is a TEST submission and will be discarded within 24 hours</INFO>
```

Expand Down
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