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planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
author nml
date Fri, 12 Sep 2025 18:50:28 +0000
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files README.md cryptogenotyper.xml images/interface_pic.png test-data/P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1 test-data/P17705_Crypto16-2R-20170927_SSUR_H12_082.ab1 test-data/P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1 test-data/P17705_gp60-Crypt14-1R-20170927_gp60R_H07_049.ab1 test-data/test_illumina_18S_F.fasta test-data/test_illumina_18S_R.fasta test-data/test_illumina_gp60_F1.fasta test-data/test_illumina_gp60_R1.fasta
diffstat 11 files changed, 366 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,6 @@
+# CryptoGenotyper
+This code allows running `CryptoGenotyper` ([https://github.com/phac-nml/CryptoGenotyper](https://github.com/phac-nml/CryptoGenotyper)) on Galaxy Project server with a convenient interface. 
+
+This wrapper provides access to complete functionality of the command line tool allowing incorporation into any workflows.
+
+![GUI](images/interface_pic.png)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cryptogenotyper.xml	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,335 @@
+<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
+  <description>
+    classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
+  </description>
+  <macros>
+   <token name="@VERSION@">1.5.0</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement>
+  </requirements>
+  <version_command>cryptogenotyper --version</version_command>
+  <command detect_errors="exit_code">
+     <![CDATA[
+
+     #set $ref_file=''
+
+     #if $db
+        ln -sf '${db}' '${db.name}' &&
+        #set $ref_file = $db.name
+     #end if
+
+     #if $primers['seqtype'] == 'contig'
+        #set $forward_name=$primers.input.forward.name.rsplit('.', 1)[0]
+        #set $reverse_name=$primers.input.reverse.name.rsplit('.', 1)[0]
+        ln -sf '${$primers.input['forward']}' '${forward_name}_forward.${primers.input.forward.ext}' &&
+        ln -sf '${$primers.input['reverse']}' '${reverse_name}_reverse.${primers.input.reverse.ext}' &&
+        cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
+        #if $db
+          --databasefile $ref_file
+        #end if
+     #else
+        #set $filename_no_ext=$primers.input.name.rsplit('.', 1)[0]
+        ln -sf '${primers.input}' '${filename_no_ext}.${primers.input.ext}' &&
+        cryptogenotyper -i './${primers.input.name}' -m '$marker' -t '$primers.seqtype'
+        #if $db
+          --databasefile $ref_file
+        #end if
+     #end if
+     $outputheader
+     -o 'result'
+     ]]>
+  </command>
+  <inputs>
+      <param name="marker" type="select" label="Marker">
+          <option value="18S">SSU rRNA (18S)</option>
+          <option value="gp60">gp60</option>
+      </param>
+      <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
+      <conditional name="primers">
+        <param name="seqtype" type="select" label="Type of Sequences">
+            <option value="forward" selected="true">Forward Only</option>
+            <option value="reverse">Reverse Only</option>
+            <option value="contig">Contig</option>
+        </param>
+        <when value="contig">
+          <param name="input" type="data_collection" collection_type="paired" format="ab1,fasta" label="Paired Sequencing File(s)"/>
+        </when>
+        <when value="forward">
+          <param name="input" type="data" format="ab1,fasta" label="Forward Sequencing File(s)"/>
+        </when>
+        <when value="reverse">
+          <param name="input" type="data" format="ab1,fasta" label="Reverse Sequencing File(s)"/>
+        </when>
+     </conditional>
+     <param name="show_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output run log?"></param>
+     <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
+     </param>
+
+
+  </inputs>
+  <outputs>
+    <!-- For single files (forward/reverse mode) -->
+    <data name="outfile_single" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" 
+     label="${tool.name} ${marker} extracted fasta from ${primers.input.name.split('.')[0]}">
+     <filter>primers['seqtype'] != 'contig'</filter>
+    </data>
+    <!-- For collections (contig mode) -->
+    <data name="outfile_collection" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" 
+          label="${tool.name} ${marker} extracted fastas">
+        <filter>primers['seqtype'] == 'contig'</filter>
+    </data>
+
+    <!-- For single files (forward/reverse mode) -->
+    <data name="outfile_report_single" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" 
+          label="${tool.name} ${marker} REPORT on ${primers.input.name.split('.')[0]}">
+        <filter>primers['seqtype'] != 'contig'</filter>
+    </data>
+    <!-- For collections (contig mode) -->
+    <data name="outfile_report_collection" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" 
+          label="${tool.name} ${marker} REPORTS">
+        <filter>primers['seqtype'] == 'contig'</filter>
+    </data>
+
+    <!-- For single files (forward/reverse mode) -->
+    <data name="outfile_log_single" format="txt" from_work_dir="cryptogenotyper.log" 
+     label="${tool.name} Run ${marker} log on ${primers.input.name.split('.')[0]}">
+      <filter>show_log and primers['seqtype'] != 'contig'</filter>
+    </data>
+    <!-- For collections (contig mode) -->
+    <data name="outfile_log_collection" format="txt" from_work_dir="cryptogenotyper.log" 
+          label="${tool.name} ${marker} logs">
+        <filter>show_log and primers['seqtype'] == 'contig'</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <!--TEST 1-->
+    <test expect_num_outputs="2">
+      <param name="marker" value="18S"/>
+      <conditional name="primers">
+            <param name="seqtype" value="forward"/>
+            <param name="input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
+      </conditional>
+      <output name="outfile_report_single" ftype="tabular">
+          <assert_contents>
+              <has_text_matching expression="C.parvum"/>
+          </assert_contents>
+      </output>
+    </test>
+    <!--TEST 2 -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="gp60"/>
+      <conditional name="primers">
+            <param name="seqtype" value="forward"/>
+            <param name="input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
+      </conditional>
+      <output name="outfile_report_single" ftype="tabular" >
+          <assert_contents>
+              <has_text_matching expression="C.parvum"/>
+          </assert_contents>
+      </output>
+    </test>
+    <!--TEST 3:Paired gp60 contig test -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="gp60"/>
+      <param name="primers|seqtype" value="contig"/>
+      <param name="primers|input">
+        <collection type="paired">
+          <element name="forward" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
+          <element name="reverse" value="P17705_gp60-Crypt14-1R-20170927_gp60R_H07_049.ab1"/>
+        </collection>
+      </param>
+      <output name="outfile_report_collection" ftype="tabular">
+        <assert_contents>
+          <has_text_matching expression="C.parvum"/>
+          <has_text_matching expression="IIaA15G2R1"/>
+        </assert_contents>
+      </output>
+    </test>
+    <!--TEST 4:Paired 18S contig test -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="18S"/>
+      <param name="primers|seqtype" value="contig"/>
+      <param name="primers|input">
+        <collection type="paired">
+          <element name="forward" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
+          <element name="reverse" value="P17705_Crypto16-2R-20170927_SSUR_H12_082.ab1"/>
+        </collection>
+      </param>
+      <output name="outfile_report_collection" ftype="tabular">
+        <assert_contents>
+          <has_text_matching expression="C.parvum"/>
+          <has_text_matching expression="Check for C. parvum TGA paralogs"/>
+        </assert_contents>
+      </output>
+    </test>
+
+ 
+    <!--TEST 5: 18S multi-fasta forward -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="18S"/>
+      <param name="primers|seqtype" value="forward"/>
+      <param name="primers|input" value="test_illumina_18S_F.fasta"/>
+      <output name="outfile_report_single" ftype="tabular">
+        <assert_contents>
+          <has_n_lines n="5"/>
+          <has_text_matching expression="C.hominis"/>
+          <has_text_matching expression="forward"/>
+        </assert_contents>
+      </output>
+    </test>
+
+    <!--TEST 6: 18S multi-fasta reverse -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="18S"/>
+      <param name="primers|seqtype" value="reverse"/>
+      <param name="primers|input" value="test_illumina_18S_R.fasta"/>
+      <output name="outfile_report_single" ftype="tabular">
+        <assert_contents>
+          <has_n_lines n="5"/>
+          <has_text_matching expression="C.hominis"/>
+          <has_text_matching expression="reverse"/>
+        </assert_contents>
+      </output>
+    </test>
+
+    <!--TEST 7: 18S multi-fasta contig -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="18S"/>
+      <param name="primers|seqtype" value="contig"/>
+      <param name="primers|input">
+        <collection type="paired">
+          <element name="forward" value="test_illumina_18S_F.fasta"/>
+          <element name="reverse" value="test_illumina_18S_R.fasta"/>
+        </collection>
+      </param>
+      <output name="outfile_report_collection" ftype="tabular">
+        <assert_contents>
+          <has_text_matching expression="C.hominis"/>
+          <has_text_matching expression="contig"/>
+        </assert_contents>
+      </output>
+    </test>
+
+    <!--TEST 8: gp60 multi-fasta forward -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="gp60"/>
+      <param name="primers|seqtype" value="forward"/>
+      <param name="primers|input" value="test_illumina_gp60_F1.fasta"/>
+      <output name="outfile_report_single" ftype="tabular">
+        <assert_contents>
+          <has_n_lines n="3"/>
+          <has_text_matching expression="C.parvum"/>
+          <has_text_matching expression="forward"/>
+          <has_text_matching expression="IIaA16G3R1"/>
+          <has_text_matching expression="IIaA15G2R2"/>
+          
+        </assert_contents>
+      </output>
+    </test>
+
+    <!--TEST 9: gp60 multi-fasta reverse -->
+    <test expect_num_outputs="2">
+      <param name="marker" value="gp60"/>
+      <param name="primers|seqtype" value="reverse"/>
+      <param name="primers|input" value="test_illumina_gp60_R1.fasta"/>
+      <output name="outfile_report_single" ftype="tabular">
+        <assert_contents>
+          <has_n_lines n="3"/>
+          <has_text_matching expression="C.parvum"/>
+          <has_text_matching expression="reverse"/>
+          <has_text_matching expression="IIaA3R1"/>
+          <has_text_matching expression="IIaA3R1"/>
+        </assert_contents>
+      </output>
+    </test>
+
+
+
+    <!--TEST 10: gp60 multi-fasta reverse -->
+     <test expect_num_outputs="3">
+      <param name="marker" value="gp60"/>
+      <param name="primers|seqtype" value="contig"/>
+      <param name="show_log" value="true"/>
+      <param name="primers|input">
+        <collection type="paired">
+          <element name="forward" value="test_illumina_gp60_F1.fasta"/>
+          <element name="reverse" value="test_illumina_gp60_R1.fasta"/>
+        </collection>
+      </param>
+      <output name="outfile_report_collection" ftype="tabular">
+        <assert_contents>
+          <has_text_matching expression="C.parvum"/>
+          <has_text_matching expression="contig"/>
+          <has_text_matching expression="IIaA16G3R1"/>
+          <has_text_matching expression="IIaA15G2R2"/>
+        </assert_contents>
+      </output>
+    </test>
+
+
+
+ 
+
+  </tests>
+
+
+  <help>
+
+
+**Syntax**
+
+CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA (18S) and gp60 markers.
+
+**❗ Important:** To process **multiple input files** and generate **a single** combined report, please import and use the workflows available `here`_.
+
+.. _here: https://github.com/phac-nml/CryptoGenotyper/tree/main/CryptoGenotyper/GalaxyWorkflows
+
+
+For a tutorial on how to use CryptoGenotyper, please refer to the `official tutorial`_.
+
+For more information, please visit https://github.com/phac-nml/CryptoGenotyper.
+
+.. _official tutorial: https://github.com/phac-nml/CryptoGenotyper/blob/docs/docs/CryptoGenotyperTutorial-CrownCopyright.pdf
+
+-----
+
+**Input:**
+
+AB1 or FASTA file(s) representing Cryptosporidium's SSU rRNA (18S) or gp60 locus can be provided as single-end reads (either forward or reverse only) or as paired-end reads in contig mode (both a forward and a reverse read for each sample).
+
+Optional: A custom reference database of SSU rRNA or gp60 locus in .fasta file format, to be used during the homology search for *Cryptosporidium* classification.
+
+
+**Output:**
+
+A tabular report and a FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample along with other relevant details. 
+The gp60 subtyping is based on the `Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`_.
+
+.. _`Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`: https://doi.org/10.1016/j.crpvbd.2025.100257
+
+  </help>
+  <citations>
+    <citation type="bibtex">
+  @ARTICLE{githubCryptoGenotyper,
+  author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.},
+  title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
+  journal = {Food and waterborne parasitology},
+  year = {2021},
+  volume = {23},
+  url = {https://doi.org/10.1016/j.fawpar.2021.e00115}
+    }</citation>
+  <citation type="bibtex">
+  @ARTICLE{RobinsonGp60,
+   author = {Robinson, Gillian and Chalmers, Rachel M. and Elwin, Kirsty and Guy, Richard A. and Bessonov, Konstantin and Troell, Kristina and Xiao, Lihua},
+   title = {Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping},
+   journal = {Current Research in Parasitology and Vector-Borne Diseases},
+   year = {2025},
+   volume = {7},
+   url = {https://doi.org/10.1016/j.crpvbd.2025.100257}
+   }
+   }</citation>
+  </citations>
+
+</tool>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_18S_F.fasta	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,8 @@
+>M04527:274:000000000-DBMY7:1:1102:16042:18930 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1101:20679:16373 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1102:12557:11653 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTAG
+>M04527:274:000000000-DBMY7:1:1102:17887:8992 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_18S_R.fasta	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,8 @@
+>M04527:274:000000000-DBMY7:1:1102:16042:18930 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1101:20679:16373 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1102:12557:11653 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTAG
+>M04527:274:000000000-DBMY7:1:1102:17887:8992 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_gp60_F1.fasta	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,5 @@
+>M04527:274:000000000-DBMY7:1:1102:14324:28396 1:N:0:26
+TCCGCTGTATTCTCAGCCCCAGCCGTTCCACTCAGAGGAACTTTAAAGGATGTTCCTGTTGAGGGCTCATCATCGTCATCGTCATCGTCATCATCATCATCATCATCATCATCATCATCATCAACATCAACCGTCGCACCAGCAAATAAGGCAAGAACTGGAGAAGACGCAGAAGGCAGTCAAGATTCTAGTGGTACTGAAGCTTCTGGTAGCCAGGGTTCTGAAGAGGAAGGTAGTGAAGACGATGGCCA
+>M04527:274:000000000-DBMY7:1:1102:20035:28200 1:N:0:26
+TCCGCTGTATTCTCAGCCCCTGCCGTTCCACTCAGAGGAACTTTAAAGGATGTTCCTGTTGAGGGCTCATCATCGTCATCGTCATCATCATCATCATCATCATCATCATCATCATCAACATCAACATCAACCGTCGCACCAGCAAATAAGGCAAGAACTGGAGAAGACGCAGAAGGCAGTCAAGATTCTAGTGGTACTGAAGCTTCTGGTAGCCAGGGTTCTGAAGAGGAAGGTAGTGAAGACGATGGCCA
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_gp60_R1.fasta	Fri Sep 12 18:50:28 2025 +0000
@@ -0,0 +1,4 @@
+>M04527:274:000000000-DBMY7:1:1102:14324:28396 2:N:0:26
+CGAACCACATTACAAATGAAGTGCCGCATTCTTCTTTTGGAGTAGCTTCTATGGTTTCGGTAGTTGCGCCTTCACTTTGAGCTGGAGTAGTGGGTTGGGAAGCAGCACTAGTTTGGCCATCGTCTTCACTACCTTCCTCTTCAGAACCCTGGCTACCAGAAGCTTCAGTACCACTAGAATCTTGACTGCCTTCTGCGTCTTCTCCAGTTCTTGCCTTATTTGCTGGTGCGACGGTTGATGTTGATGATGAT
+>M04527:274:000000000-DBMY7:1:1102:20035:28200 2:N:0:26
+CGAACCACATTACAAATGAAGTGCCGCATTCTTCTTTTGGAGTAGCTTCTATGGTTTCGGTAGTTGCGCCTTCACTTTGAGCTGGAGTAGTGGGTTGGGAAGCAGCACTAGTTTGGCCATCGTCTTCACTACCTTCCTCTTCAGAACCCTGGCTACCAGAAGCTTCAGTACCACTAGAATCTTGACTGCCTTCTGCGTCTTCTCCAGTTCTTGCCTTATTTGCTGGTGCGACGGTTGATGTTGATGTTGAT
\ No newline at end of file