On Thu, Nov 7, 2013 at 3:18 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Nov 7, 2013 at 12:21 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>>
>> Related to this, would people prefer if the $on_string in the case of
>> a single input file was the input file's name (e.g. "My Genes") rather
>> than "data 1"? (When there are multiple input files, $on_string needs
>> to be kept short).
>
> That turned out to be quite an easy change (patch below), and
> personally I think this makes the $on_string much nicer.
>
> Peter
Getting back to my motivating example, since fasta_to_tabular.xml
does not give the output a label and depends on the default, the
small change to $on_string should result in the conversion of a
file named "My Genes" as "FASTA-to-Tabular on My Genes",
rather than "FASTA-to-Tabular on data 1" as now.
Here's another variant to keep the "data 1" text in $on_string,
if people are attached to this functionality. That would result in
"FASTA-to-Tabular on data 1 (My Genes)".
Also, here's an outline patch to explicitly produce my preferred
label of "My Genes (as tabular)" etc.
(Bjoern is right though - a more long term solution is needed to
better address naming, like the tag idea on Trello.)
Peter
------------------------------------------------------------------------------------------
$ hg diff lib/galaxy/tools/actions/__init__.py
diff -r 77d58fdd1c2e lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py Tue Oct 29 14:21:48 2013 -0400
+++ b/lib/galaxy/tools/actions/__init__.py Thu Nov 07 15:49:15 2013 +0000
@@ -181,6 +181,7 @@
input_names = []
input_ext = 'data'
input_dbkey = incoming.get( "dbkey", "?" )
+ on_text = ''
for name, data in inp_data.items():
if not data:
data = NoneDataset( datatypes_registry =
trans.app.datatypes_registry )
@@ -194,6 +195,8 @@
else: # HDA
if data.hid:
input_names.append( 'data %s' % data.hid )
+ #Will use this on_text if only one input dataset:
+ on_text = "data %s (%s)" % (data.id, data.name)
input_ext = data.ext
if data.dbkey not in [None, '?']:
@@ -230,7 +233,10 @@
output_permissions =
trans.app.security_agent.history_get_default_permissions( history )
# Build name for output datasets based on tool name and input names
if len( input_names ) == 1:
- on_text = input_names[0]
+ #We recorded the dataset name as on_text earlier...
+ if not on_text:
+ #Fall back on the shorter 'data %i' style:
+ on_text = input_names[0]
elif len( input_names ) == 2:
on_text = '%s and %s' % tuple(input_names[0:2])
elif len( input_names ) == 3:
------------------------------------------------------------------------------------------
$ hg diff tools
diff -r 77d58fdd1c2e tools/fasta_tools/fasta_to_tabular.xml
--- a/tools/fasta_tools/fasta_to_tabular.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/fasta_tools/fasta_to_tabular.xml Thu Nov 07 15:42:13 2013 +0000
@@ -11,7 +11,7 @@
</param>
</inputs>
<outputs>
- <data name="output" format="tabular"/>
+ <data name="output" format="tabular"
label="$input.display_name (as tabular)"/>
</outputs>
<tests>
<test>
diff -r 77d58fdd1c2e tools/fasta_tools/tabular_to_fasta.xml
--- a/tools/fasta_tools/tabular_to_fasta.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/fasta_tools/tabular_to_fasta.xml Thu Nov 07 15:42:13 2013 +0000
@@ -7,7 +7,7 @@
<param name="seq_col" type="data_column" data_ref="input"
numerical="False" label="Sequence column" />
</inputs>
<outputs>
- <data name="output" format="fasta"/>
+ <data name="output" format="fasta" label="$input.display_name
(as FASTA)" />
</outputs>
<tests>
<test>
@@ -40,4 +40,4 @@
GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
</help>
-</tool>
\ No newline at end of file
+</tool>
diff -r 77d58fdd1c2e tools/fastq/fastq_to_fasta.xml
--- a/tools/fastq/fastq_to_fasta.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/fastq/fastq_to_fasta.xml Thu Nov 07 15:42:13 2013 +0000
@@ -5,7 +5,7 @@
<param name="input_file" type="data" format="fastq" label="FASTQ
file to convert" />
</inputs>
<outputs>
- <data name="output_file" format="fasta" />
+ <data name="output_file" format="fasta" label="$input_file.name
(as FASTA)" />
</outputs>
<tests>
<!-- basic test -->
diff -r 77d58fdd1c2e tools/fastq/fastq_to_tabular.xml
--- a/tools/fastq/fastq_to_tabular.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/fastq/fastq_to_tabular.xml Thu Nov 07 15:42:13 2013 +0000
@@ -8,7 +8,7 @@
</param>
</inputs>
<outputs>
- <data name="output_file" format="tabular" />
+ <data name="output_file" format="tabular" label="$input_file.name
(as tabular)" />
</outputs>
<tests>
<!-- basic test -->
diff -r 77d58fdd1c2e tools/fastq/tabular_to_fastq.xml
--- a/tools/fastq/tabular_to_fastq.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/fastq/tabular_to_fastq.xml Thu Nov 07 15:42:13 2013 +0000
@@ -8,7 +8,7 @@
<param name="quality" label="Quality column" type="data_column"
data_ref="input_file" />
</inputs>
<outputs>
- <data name="output_file" format="fastq" />
+ <data name="output_file" format="fastq" label="$input_file.name
(as FASTQ)" />
</outputs>
<tests>
<!-- basic test -->
diff -r 77d58fdd1c2e tools/filters/axt_to_concat_fasta.xml
--- a/tools/filters/axt_to_concat_fasta.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/filters/axt_to_concat_fasta.xml Thu Nov 07 15:42:13 2013 +0000
@@ -14,7 +14,7 @@
<param name="axt_input" value="1.axt" ftype="axt" />
<param name="dbkey_1" value='hg17' />
<param name="dbkey_2" value="panTro1" />
- <output name="out_file1" file="axt_to_concat_fasta.dat" />
+ <output name="out_file1" file="axt_to_concat_fasta.dat"
label="$axt_input.name (as FASTA)"/>
</test>
</tests>
<help>
diff -r 77d58fdd1c2e tools/filters/wig_to_bigwig.xml
--- a/tools/filters/wig_to_bigwig.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/filters/wig_to_bigwig.xml Thu Nov 07 15:42:13 2013 +0000
@@ -29,7 +29,7 @@
</conditional>
</inputs>
<outputs>
- <data format="bigwig" name="out_file1" />
+ <data format="bigwig" name="out_file1" label="$input1.name (as bigwig)" />
</outputs>
<tests>
<test>
diff -r 77d58fdd1c2e tools/filters/wiggle_to_simple.xml
--- a/tools/filters/wiggle_to_simple.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/filters/wiggle_to_simple.xml Thu Nov 07 15:42:13 2013 +0000
@@ -5,7 +5,7 @@
<param format="wig" name="input" type="data" label="Convert"/>
</inputs>
<outputs>
- <data format="interval" name="out_file1" />
+ <data format="interval" name="out_file1" label="$input.name (as
interval)" />
</outputs>
<tests>
<test>
diff -r 77d58fdd1c2e tools/stats/wiggle_to_simple.xml
--- a/tools/stats/wiggle_to_simple.xml Tue Oct 29 14:21:48 2013 -0400
+++ b/tools/stats/wiggle_to_simple.xml Thu Nov 07 15:42:13 2013 +0000
@@ -5,7 +5,7 @@
<param format="wig" name="input" type="data" label="Convert"/>
</inputs>
<outputs>
- <data format="interval" name="out_file1" />
+ <data format="interval" name="out_file1" label="$input.name (as
interval)" />
</outputs>
<tests>
<test>
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