diff preprocess.xml @ 12:613b7551f28b draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0c3aee486a7e9b369ad4c037c2f588236acad117-dirty

--- a/preprocess.xml	Fri May 13 15:33:27 2022 +0000
+++ b/preprocess.xml	Mon May 16 14:19:09 2022 +0000
@@ -233,7 +233,7 @@
     </inputs>
     <outputs>
         <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" />
-        <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
+        <data format="tsv" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
         <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
     </outputs>
     <tests>
@@ -340,7 +340,7 @@
    :Files: One sequence file by sample (format `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_)
    :Example: splA.fastq.gz,  splB.fastq.gz
 
-Remark: In an archive, if you use R1 and R2 files, their names must end with *_R1* and *_R2*. The part upstream from this tag (_R1 and _R2) will be consider as sample name.
+Remark: In an archive, if you use R1 and R2 files, their names must end with *_R1* and *_R2*. The upstream part from this tag (_R1 and _R2) will be consider as sample name.
 
 .. class:: h3
 
@@ -348,7 +348,7 @@
 
 **Sequence file** (dereplicated.fasta):
 
- Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). These sequences are dereplicated: strictly identical sequences are represented only once, the initial count by sample is kept in count file (see bellow) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to un-merged pair sequence if you want to keep them.
+ Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). These sequences are dereplicated: strictly identical sequences are represented only once, the initial count by sample is kept in count file (see bellow) and the total count is added in the sequence header. A "FROGS_combined" suffix will be added to un-merged pair sequences if you want to keep them.
 
 **Count file** (count.tsv):
 
@@ -392,6 +392,7 @@
 Keeping or not un-merged paired reads
 
 .. class:: warningmark
+
 This option is usefull when and only when, **targeted amplicon is longer than the sequencing technology** can provide (ITS amplicons, V1-V4 region of 16S for example). In other case, carefully, you will only keep noise in your analysis.
 
 .. class:: h3